chr6-31710997-G-A

Variant summary

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

The ENST00000503322.1(LY6G6F-LY6G6D):​c.802+816G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,016 control chromosomes in the GnomAD database, including 638 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 0.077 ( 638 hom., cov: 31)

Consequence

LY6G6F-LY6G6D
ENST00000503322.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.777
Variant links:
Genes affected
LY6G6F-LY6G6D (HGNC:38821): (LY6G6F-LY6G6D readthrough) This locus represents naturally occurring readthrough transcription between the neighboring LY6G6F (lymphocyte antigen 6 family member G6F) and LY6G6D (lymphocyte antigen 6 family member G6D) genes on chromosome 6. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jul 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LY6G6F-LY6G6DNM_001353334.2 linkuse as main transcriptc.802+816G>A intron_variant NP_001340263.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
LY6G6F-LY6G6DENST00000503322.1 linkuse as main transcriptc.802+816G>A intron_variant 1 ENSP00000421232.1
ENSG00000204422ENST00000461287.1 linkuse as main transcriptn.537+1020C>T intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0771
AC:
11712
AN:
151898
Hom.:
637
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.141
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.0969
Gnomad ASJ
AF:
0.0435
Gnomad EAS
AF:
0.00270
Gnomad SAS
AF:
0.00621
Gnomad FIN
AF:
0.00500
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0585
Gnomad OTH
AF:
0.0831
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0770
AC:
11711
AN:
152016
Hom.:
638
Cov.:
31
AF XY:
0.0729
AC XY:
5421
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.140
Gnomad4 AMR
AF:
0.0969
Gnomad4 ASJ
AF:
0.0435
Gnomad4 EAS
AF:
0.00270
Gnomad4 SAS
AF:
0.00601
Gnomad4 FIN
AF:
0.00500
Gnomad4 NFE
AF:
0.0585
Gnomad4 OTH
AF:
0.0817
Alfa
AF:
0.0597
Hom.:
166
Bravo
AF:
0.0897
Asia WGS
AF:
0.0110
AC:
39
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
7.3
DANN
Benign
0.45

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: rs6916278; hg19: chr6-31678774; API