rs2675661

Variant names:

• chr10-73946219-T-G
• rs2675661

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 0.111 in 152,022 control chromosomes in the GnomAD database, including 1,397 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 0.11 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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: 0.110 AC: 16775 AN: 151904 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.0596

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.111 AC: 16806 AN: 152022 Hom.: 1397 Cov.: 32 AF XY: 0.111 AC XY: 8248 AN XY: 74322

African (AFR) AF: 0.148 AC: 6130 AN: 41442

American (AMR) AF: 0.224 AC: 3415 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0596 AC: 207 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1792 AN: 5156

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4820

European-Finnish (FIN) AF: 0.0671 AC: 709 AN: 10560

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3845 AN: 67996

Other (OTH) AF: 0.121 AC: 256 AN: 2110

Alfa AF: 0.0881 Hom.: 1478

Bravo AF: 0.129

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs2675661; hg19: chr10-75705977; COSMIC: COSV68663840;