NM_173683.4:c.962-7229G>C

Variant names:

• chr8-10906145-C-G
• rs4326350
• NM_173683.4:c.962-7229G>C

Variant summary

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

The NM_173683.4(XKR6):​c.962-7229G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,050 control chromosomes in the GnomAD database, including 19,067 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 0.48 (19067 hom., cov: 33)
• Consequence: XKR6 NM_173683.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 13 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173683.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	NM_173683.4	MANE Select	c.962-7229G>C		intron	N/A	NP_775954.2	Q5GH73-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	XKR6	ENST00000416569.3	TSL:1 MANE Select	c.962-7229G>C		intron	N/A	ENSP00000416707.2	Q5GH73-1
	XKR6	ENST00000382461.8	TSL:1	c.185-7229G>C		intron	N/A	ENSP00000371900.4	H7BYF9

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73366 AN: 151932 Hom.: 19045 Cov.: 33

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.0217

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.483 AC: 73425 AN: 152050 Hom.: 19067 Cov.: 33 AF XY: 0.471 AC XY: 35026 AN XY: 74344

African (AFR) AF: 0.626 AC: 25954 AN: 41444

American (AMR) AF: 0.349 AC: 5332 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5190

South Asian (SAS) AF: 0.396 AC: 1908 AN: 4820

European-Finnish (FIN) AF: 0.353 AC: 3738 AN: 10576

Middle Eastern (MID) AF: 0.538 AC: 156 AN: 290

European-Non Finnish (NFE) AF: 0.484 AC: 32918 AN: 67960

Other (OTH) AF: 0.457 AC: 967 AN: 2114

Alfa AF: 0.511 Hom.: 2550

Bravo AF: 0.483

Asia WGS AF: 0.255 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.35
PhyloP100		-0.78
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: rs4326350; hg19: chr8-10763655;