Variant chr7-6035813-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The ENST00000199389.11(EIF2AK1):c.1332+1611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00302 in 1,550,174 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0031 ( 21 hom. )

Consequence

EIF2AK1
ENST00000199389.11 intron

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.807

Variant links:

Genes affected

ANKRD61 (HGNC:22467): (ankyrin repeat domain 61) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD61 links:

EIF2AK1 (HGNC:24921): (eukaryotic translation initiation factor 2 alpha kinase 1) The protein encoded by this gene acts at the level of translation initiation to downregulate protein synthesis in response to stress. The encoded protein is a kinase that can be inactivated by hemin. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

EIF2AK1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 7-6035813-C-T is Benign according to our data. Variant chr7-6035813-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657295.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 327 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD61	NM_001271700.2 linkuse as main transcript	c.684C>T	p.Asn228Asn	synonymous_variant	3/3	ENST00000409061.2	NP_001258629.1	A6NGH8
EIF2AK1	NM_014413.4 linkuse as main transcript	c.1332+1611G>A		intron_variant		ENST00000199389.11	NP_055228.2	Q9BQI3-1A0A024QZU1
EIF2AK1	NM_001134335.2 linkuse as main transcript	c.1329+1611G>A		intron_variant			NP_001127807.1	Q9BQI3-2
EIF2AK1	XM_047420200.1 linkuse as main transcript	c.708+1611G>A		intron_variant			XP_047276156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD61	ENST00000409061.2 linkuse as main transcript	c.684C>T	p.Asn228Asn	synonymous_variant	3/3	5	NM_001271700.2	ENSP00000386502.1		A6NGH8
EIF2AK1	ENST00000199389.11 linkuse as main transcript	c.1332+1611G>A		intron_variant		1	NM_014413.4	ENSP00000199389.6		Q9BQI3-1

Frequencies

GnomAD3 genomes

AF:

0.00215

AC:

327

AN:

152196

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000917

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00744

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00319

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00209

AC:

313

AN:

149760

Hom.:

AF XY:

0.00196

AC XY:

157

AN XY:

80252

show subpopulations

Gnomad AFR exome

AF:

0.000283

Gnomad AMR exome

AF:

0.00118

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000186

Gnomad SAS exome

AF:

0.000758

Gnomad FIN exome

AF:

0.00454

Gnomad NFE exome

AF:

0.00319

Gnomad OTH exome

AF:

0.00228

GnomAD4 exome

AF:

0.00312

AC:

4355

AN:

1397860

Hom.:

Cov.:

AF XY:

0.00301

AC XY:

2073

AN XY:

689284

show subpopulations

Gnomad4 AFR exome

AF:

0.000697

Gnomad4 AMR exome

AF:

0.00121

Gnomad4 ASJ exome

AF:

0.0000397

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000808

Gnomad4 FIN exome

AF:

0.00637

Gnomad4 NFE exome

AF:

0.00349

Gnomad4 OTH exome

AF:

0.00263

GnomAD4 genome

AF:

0.00215

AC:

327

AN:

152314

Hom.:

Cov.:

AF XY:

0.00219

AC XY:

163

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.000361

Gnomad4 AMR

AF:

0.000916

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00744

Gnomad4 NFE

AF:

0.00319

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00262

Hom.:

Bravo

AF:

0.00173

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

ANKRD61: BP4 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over