chr2-97113736-G-C

Position:

• chr2-97113736-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001354587.1(ANKRD36):​c.-4G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00125 in 1,608,458 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0022 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0011 (25 hom.)
• Consequence: ANKRD36 NM_001354587.1 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200

Genes affected

ANKRD36 (HGNC:24079): (ankyrin repeat domain 36)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 2-97113736-G-C is Benign according to our data. Variant chr2-97113736-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2651154.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD36	NM_001354587.1	c.-4G>C		5_prime_UTR_variant	1/76	ENST00000420699.9	NP_001341516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ANKRD36	ENST00000420699.9	c.-4G>C		5_prime_UTR_variant	1/76	5	NM_001354587.1	ENSP00000391950	P1
ANKRD36	ENST00000452478.2	n.185G>C		non_coding_transcript_exon_variant	1/3	1
ANKRD36	ENST00000461153.7	c.-4G>C		5_prime_UTR_variant	1/75	5		ENSP00000419530	P1
ANKRD36	ENST00000652721.1	c.-4G>C		5_prime_UTR_variant	1/76			ENSP00000498611	P1

Frequencies

GnomAD3 genomes AF: 0.00224 AC: 336 AN: 150278 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.000556

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00304

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000199

Gnomad SAS AF: 0.00105

Gnomad FIN AF: 0.000914

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00352

Gnomad OTH AF: 0.00433

GnomAD3 exomes AF: 0.000637 AC: 157 AN: 246496 Hom.: 3 AF XY: 0.000596 AC XY: 80 AN XY: 134188

Gnomad AFR exome AF: 0.0000651

Gnomad AMR exome AF: 0.000967

Gnomad ASJ exome AF: 0.0000999

Gnomad EAS exome AF: 0.000113

Gnomad SAS exome AF: 0.000164

Gnomad FIN exome AF: 0.000142

Gnomad NFE exome AF: 0.000966

Gnomad OTH exome AF: 0.000669

GnomAD4 exome AF: 0.00115 AC: 1673 AN: 1458080 Hom.: 25 Cov.: 31 AF XY: 0.00121 AC XY: 874 AN XY: 725296

Gnomad4 AFR exome AF: 0.000120

Gnomad4 AMR exome AF: 0.00162

Gnomad4 ASJ exome AF: 0.000153

Gnomad4 EAS exome AF: 0.0000767

Gnomad4 SAS exome AF: 0.000628

Gnomad4 FIN exome AF: 0.000680

Gnomad4 NFE exome AF: 0.00120

Gnomad4 OTH exome AF: 0.00211

GnomAD4 genome AF: 0.00223 AC: 336 AN: 150378 Hom.: 4 Cov.: 32 AF XY: 0.00209 AC XY: 153 AN XY: 73268

Gnomad4 AFR AF: 0.000554

Gnomad4 AMR AF: 0.00303

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000200

Gnomad4 SAS AF: 0.00105

Gnomad4 FIN AF: 0.000914

Gnomad4 NFE AF: 0.00352

Gnomad4 OTH AF: 0.00432

Alfa AF: 0.00113 Hom.: 1

Bravo AF: 0.00264

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

ANKRD36: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs201655336; hg19: chr2-97779473;