rs10503672

Variant names:

• chr8-20130192-C-T
• rs10503672
• XR_949563.2:n.3400+273C>T

Variant summary

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

The XR_949563.2(LOC105379312):​n.3400+273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,108 control chromosomes in the GnomAD database, including 3,743 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 0.19 (3743 hom., cov: 32)
• Consequence: LOC105379312 XR_949563.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 4 publications found

Genes affected

LOC105379312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 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: 0.194 AC: 29534 AN: 151988 Hom.: 3744 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.194 AC: 29524 AN: 152108 Hom.: 3743 Cov.: 32 AF XY: 0.198 AC XY: 14708 AN XY: 74354

African (AFR) AF: 0.0509 AC: 2113 AN: 41518

American (AMR) AF: 0.227 AC: 3470 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.0570 AC: 295 AN: 5176

South Asian (SAS) AF: 0.158 AC: 759 AN: 4814

European-Finnish (FIN) AF: 0.359 AC: 3795 AN: 10570

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17574 AN: 67958

Other (OTH) AF: 0.216 AC: 456 AN: 2110

Alfa AF: 0.231 Hom.: 11194

Bravo AF: 0.179

Asia WGS AF: 0.121 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		0.012

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10503672;

hg19: chr8-19987703;