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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379312	XR_949563.2	n.3400+273C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs10503672; hg19: chr8-19987703;