rs1503814

Variant names:

• chr1-161739329-C-T
• rs1503814

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 0.682 in 152,130 control chromosomes in the GnomAD database, including 36,150 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 0.68 (36150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 18 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 (NFE) allele frequency at 95% confidence interval = 0.738 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: 0.682 AC: 103647 AN: 152012 Hom.: 36135 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.682 AC: 103698 AN: 152130 Hom.: 36150 Cov.: 32 AF XY: 0.680 AC XY: 50569 AN XY: 74374

African (AFR) AF: 0.627 AC: 26006 AN: 41494

American (AMR) AF: 0.585 AC: 8936 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1700 AN: 5184

South Asian (SAS) AF: 0.635 AC: 3056 AN: 4816

European-Finnish (FIN) AF: 0.803 AC: 8504 AN: 10588

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50565 AN: 67982

Other (OTH) AF: 0.703 AC: 1484 AN: 2112

Alfa AF: 0.700 Hom.: 9958

Bravo AF: 0.660

Asia WGS AF: 0.469 AC: 1632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.095
DANN	Benign	0.52
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1503814; hg19: chr1-161709119;