Variant 8-6812110-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_207411.5(XKR5):c.1149C>T(p.Val383Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,546,518 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0012 ( 4 hom. )

Consequence

XKR5
NM_207411.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.597

Variant links:

Genes affected

XKR5 (HGNC:20782): (XK related 5) Predicted to be involved in apoptotic process involved in development; engulfment of apoptotic cell; and phosphatidylserine exposure on apoptotic cell surface. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

XKR5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 8-6812110-G-A is Benign according to our data. Variant chr8-6812110-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2658352.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.597 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
XKR5	NM_207411.5 linkuse as main transcript	c.1149C>T	p.Val383Val	synonymous_variant	7/7	ENST00000618742.3	NP_997294.3	Q6UX68-1
XKR5	NM_001289973.2 linkuse as main transcript	c.660C>T	p.Val220Val	synonymous_variant	8/8		NP_001276902.1	Q6UX68

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
XKR5	ENST00000618742.3 linkuse as main transcript	c.1149C>T	p.Val383Val	synonymous_variant	7/7	1	NM_207411.5	ENSP00000483879.1	Q6UX68-1
XKR5	ENST00000618990.4 linkuse as main transcript	n.*1026C>T		non_coding_transcript_exon_variant	8/8	1		ENSP00000485506.1	Q6UX68-3
XKR5	ENST00000618990.4 linkuse as main transcript	n.*1026C>T		3_prime_UTR_variant	8/8	1		ENSP00000485506.1	Q6UX68-3

Frequencies

GnomAD3 genomes

AF:

0.00341

AC:

519

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00907

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00268

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000999

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00180

AC:

275

AN:

152750

Hom.:

AF XY:

0.00159

AC XY:

129

AN XY:

81128

show subpopulations

Gnomad AFR exome

AF:

0.00918

Gnomad AMR exome

AF:

0.00272

Gnomad ASJ exome

AF:

0.00611

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000440

Gnomad FIN exome

AF:

0.0000739

Gnomad NFE exome

AF:

0.00114

Gnomad OTH exome

AF:

0.00298

GnomAD4 exome

AF:

0.00124

AC:

1722

AN:

1394192

Hom.:

Cov.:

AF XY:

0.00115

AC XY:

790

AN XY:

687848

show subpopulations

Gnomad4 AFR exome

AF:

0.00915

Gnomad4 AMR exome

AF:

0.00314

Gnomad4 ASJ exome

AF:

0.00473

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.0000757

Gnomad4 FIN exome

AF:

0.000385

Gnomad4 NFE exome

AF:

0.000953

Gnomad4 OTH exome

AF:

0.00223

GnomAD4 genome

AF:

0.00341

AC:

520

AN:

152326

Hom.:

Cov.:

AF XY:

0.00346

AC XY:

258

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00905

Gnomad4 AMR

AF:

0.00268

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.000999

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00113

Hom.:

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

Apr 01, 2023

XKR5: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.12

DANN

Benign

0.41

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