rs10263639

Variant names:

• chr7-67594280-T-C
• rs10263639
• XR_001745238.2:n.163+8031A>G

Variant summary

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

The XR_001745238.2(LOC105375340):​n.163+8031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,146 control chromosomes in the GnomAD database, including 2,376 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 0.17 (2376 hom., cov: 32)
• Consequence: LOC105375340 XR_001745238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 15 publications found

Genes affected

LOC105375340 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25858 AN: 152028 Hom.: 2371 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.170 AC: 25883 AN: 152146 Hom.: 2376 Cov.: 32 AF XY: 0.170 AC XY: 12616 AN XY: 74398

African (AFR) AF: 0.191 AC: 7917 AN: 41492

American (AMR) AF: 0.247 AC: 3771 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3472

East Asian (EAS) AF: 0.0851 AC: 440 AN: 5172

South Asian (SAS) AF: 0.117 AC: 565 AN: 4816

European-Finnish (FIN) AF: 0.135 AC: 1434 AN: 10602

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10565 AN: 67994

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.158 Hom.: 7157

Bravo AF: 0.178

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		-0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10263639; hg19: chr7-67059267; COSMIC: COSV54093349;