rs17782554

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173683.4(XKR6):​c.764+35980C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,124 control chromosomes in the GnomAD database, including 7,298 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 0.28 ( 7298 hom., cov: 33)

Consequence

XKR6
NM_173683.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.479
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
XKR6NM_173683.4 linkuse as main transcriptc.764+35980C>G intron_variant ENST00000416569.3 NP_775954.2 Q5GH73-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
XKR6ENST00000416569.3 linkuse as main transcriptc.764+35980C>G intron_variant 1 NM_173683.4 ENSP00000416707.2 Q5GH73-1
XKR6ENST00000529336.1 linkuse as main transcriptn.257+35980C>G intron_variant 3 ENSP00000436594.1 H0YEU9

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42782
AN:
152006
Hom.:
7299
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.141
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.210
Gnomad ASJ
AF:
0.462
Gnomad EAS
AF:
0.00385
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.341
Gnomad MID
AF:
0.396
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.301
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42775
AN:
152124
Hom.:
7298
Cov.:
33
AF XY:
0.274
AC XY:
20368
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.140
Gnomad4 AMR
AF:
0.209
Gnomad4 ASJ
AF:
0.462
Gnomad4 EAS
AF:
0.00386
Gnomad4 SAS
AF:
0.202
Gnomad4 FIN
AF:
0.341
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.298
Alfa
AF:
0.360
Hom.:
1386
Bravo
AF:
0.262
Asia WGS
AF:
0.106
AC:
372
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.6
DANN
Benign
0.76

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.

Other links and lift over

dbSNP: rs17782554; hg19: chr8-11022106; API