rs4103781

Variant names:

• chr1-154308146-C-T
• rs4103781

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 0.529 in 151,944 control chromosomes in the GnomAD database, including 21,647 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 0.53 (21647 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.614 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: 0.528 AC: 80237 AN: 151826 Hom.: 21619 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.529 AC: 80310 AN: 151944 Hom.: 21647 Cov.: 31 AF XY: 0.529 AC XY: 39316 AN XY: 74270

African (AFR) AF: 0.620 AC: 25688 AN: 41424

American (AMR) AF: 0.446 AC: 6787 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1781 AN: 5166

South Asian (SAS) AF: 0.506 AC: 2437 AN: 4820

European-Finnish (FIN) AF: 0.547 AC: 5762 AN: 10540

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34897 AN: 67978

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.511 Hom.: 9298

Bravo AF: 0.520

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.85
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4103781; hg19: chr1-154280622;