rs776052

Variant names:

• chr1-37713471-C-T
• rs776052

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 0.232 in 149,552 control chromosomes in the GnomAD database, including 4,221 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 0.23 (4221 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.232 AC: 34740 AN: 149466 Hom.: 4223 Cov.: 28

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.232 AC: 34737 AN: 149552 Hom.: 4221 Cov.: 28 AF XY: 0.228 AC XY: 16580 AN XY: 72790

African (AFR) AF: 0.230 AC: 9331 AN: 40520

American (AMR) AF: 0.179 AC: 2689 AN: 14986

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 932 AN: 3458

East Asian (EAS) AF: 0.0246 AC: 127 AN: 5154

South Asian (SAS) AF: 0.167 AC: 774 AN: 4646

European-Finnish (FIN) AF: 0.244 AC: 2447 AN: 10014

Middle Eastern (MID) AF: 0.285 AC: 82 AN: 288

European-Non Finnish (NFE) AF: 0.260 AC: 17558 AN: 67510

Other (OTH) AF: 0.224 AC: 465 AN: 2074

Alfa AF: 0.250 Hom.: 6238

Bravo AF: 0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.17
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs776052; hg19: chr1-38179143; COSMIC: COSV57622138;