rs10505672

Variant names:

• chr8-137261619-G-A
• rs10505672

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 0.182 in 152,076 control chromosomes in the GnomAD database, including 2,641 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 0.18 (2641 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.182 AC: 27681 AN: 151958 Hom.: 2634 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0459

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.182 AC: 27708 AN: 152076 Hom.: 2641 Cov.: 33 AF XY: 0.183 AC XY: 13578 AN XY: 74372

African (AFR) AF: 0.219 AC: 9081 AN: 41496

American (AMR) AF: 0.131 AC: 2005 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.0458 AC: 237 AN: 5176

South Asian (SAS) AF: 0.148 AC: 717 AN: 4830

European-Finnish (FIN) AF: 0.216 AC: 2284 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12293 AN: 67964

Other (OTH) AF: 0.156 AC: 329 AN: 2112

Alfa AF: 0.175 Hom.: 1337

Bravo AF: 0.176

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	11
DANN	Benign	0.44
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs10505672; hg19: chr8-138273862; COSMIC: COSV68352662;