rs3753503

Variant names:

• chr1-7781911-G-A
• rs3753503

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 0.213 in 151,968 control chromosomes in the GnomAD database, including 3,846 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 0.21 (3846 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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: 0.213 AC: 32303 AN: 151848 Hom.: 3845 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.0826

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32323 AN: 151968 Hom.: 3846 Cov.: 32 AF XY: 0.208 AC XY: 15468 AN XY: 74290

African (AFR) AF: 0.283 AC: 11726 AN: 41394

American (AMR) AF: 0.161 AC: 2463 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1897 AN: 5152

South Asian (SAS) AF: 0.298 AC: 1436 AN: 4818

European-Finnish (FIN) AF: 0.0826 AC: 873 AN: 10568

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12380 AN: 67974

Other (OTH) AF: 0.211 AC: 445 AN: 2110

Alfa AF: 0.206 Hom.: 526

Bravo AF: 0.220

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.89
DANN	Benign	0.79
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs3753503; hg19: chr1-7841971;