rs10507671

Variant names:

• chr13-61618498-A-G
• rs10507671

Your query was ambiguous. Multiple possible variants found:

• chr13-61618498-A-G
• chr13-61618498-A-T

Variant summary

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

The variant allele was found at a frequency of 0.16 in 151,772 control chromosomes in the GnomAD database, including 2,149 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 0.16 (2149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24279 AN: 151654 Hom.: 2137 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.160 AC: 24318 AN: 151772 Hom.: 2149 Cov.: 32 AF XY: 0.163 AC XY: 12112 AN XY: 74210

African (AFR) AF: 0.225 AC: 9320 AN: 41460

American (AMR) AF: 0.114 AC: 1726 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3460

East Asian (EAS) AF: 0.202 AC: 1042 AN: 5148

South Asian (SAS) AF: 0.117 AC: 564 AN: 4816

European-Finnish (FIN) AF: 0.195 AC: 2058 AN: 10580

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8706 AN: 67800

Other (OTH) AF: 0.141 AC: 297 AN: 2112

Alfa AF: 0.0814 Hom.: 2027

Bravo AF: 0.158

Asia WGS AF: 0.135 AC: 471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.88
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs10507671; hg19: chr13-62192631;