rs3885690

Variant names:

• chr8-10969359-T-C
• rs3885690
• NM_173683.4:c.765-44529A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-10969359-T-C
• chr8-10969359-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173683.4(XKR6):​c.765-44529A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,092 control chromosomes in the GnomAD database, including 8,622 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (8622 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 10 publications found

Genes affected

XKR6 (HGNC:27806): (XK related 6) 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
XKR6	NM_173683.4	c.765-44529A>G		intron_variant	Intron 1 of 2	ENST00000416569.3	NP_775954.2
XKR6	XM_024447129.2	c.765-44529A>G		intron_variant	Intron 1 of 2		XP_024302897.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
XKR6	ENST00000416569.3	c.765-44529A>G		intron_variant	Intron 1 of 2	1	NM_173683.4	ENSP00000416707.2
XKR6	ENST00000382461.8	c.-14+33029A>G		intron_variant	Intron 1 of 2	1		ENSP00000371900.4

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50282 AN: 151974 Hom.: 8626 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.330

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.331 AC: 50284 AN: 152092 Hom.: 8622 Cov.: 33 AF XY: 0.322 AC XY: 23929 AN XY: 74348

African (AFR) AF: 0.312 AC: 12960 AN: 41480

American (AMR) AF: 0.302 AC: 4614 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3470

East Asian (EAS) AF: 0.132 AC: 685 AN: 5176

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3132 AN: 10588

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24970 AN: 67962

Other (OTH) AF: 0.328 AC: 693 AN: 2110

Alfa AF: 0.340 Hom.: 6160

Bravo AF: 0.329

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3885690; hg19: chr8-10826869;