rs7261610

Variant names:

• chr20-39881734-C-T
• rs7261610

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 0.329 in 151,854 control chromosomes in the GnomAD database, including 9,173 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 0.33 (9173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 5 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.329 AC: 49866 AN: 151736 Hom.: 9163 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.0986

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.329 AC: 49918 AN: 151854 Hom.: 9173 Cov.: 32 AF XY: 0.328 AC XY: 24340 AN XY: 74216

African (AFR) AF: 0.501 AC: 20738 AN: 41382

American (AMR) AF: 0.221 AC: 3370 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0986 AC: 342 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1288 AN: 5152

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4816

European-Finnish (FIN) AF: 0.376 AC: 3955 AN: 10532

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

European-Non Finnish (NFE) AF: 0.269 AC: 18296 AN: 67940

Other (OTH) AF: 0.259 AC: 547 AN: 2108

Alfa AF: 0.279 Hom.: 20178

Bravo AF: 0.325

Asia WGS AF: 0.244 AC: 850 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	5.3
DANN	Benign	0.31
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7261610; hg19: chr20-38510376;