rs4951003

Variant names:

• chr1-205492939-C-T
• rs4951003

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 0.238 in 151,940 control chromosomes in the GnomAD database, including 4,736 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 0.24 (4736 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.238 AC: 36123 AN: 151822 Hom.: 4733 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.238 AC: 36133 AN: 151940 Hom.: 4736 Cov.: 31 AF XY: 0.238 AC XY: 17671 AN XY: 74266

African (AFR) AF: 0.175 AC: 7259 AN: 41414

American (AMR) AF: 0.210 AC: 3211 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1445 AN: 3472

East Asian (EAS) AF: 0.0327 AC: 169 AN: 5168

South Asian (SAS) AF: 0.379 AC: 1821 AN: 4802

European-Finnish (FIN) AF: 0.229 AC: 2417 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18715 AN: 67928

Other (OTH) AF: 0.263 AC: 554 AN: 2110

Alfa AF: 0.254 Hom.: 7568

Bravo AF: 0.229

Asia WGS AF: 0.191 AC: 664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4951003; hg19: chr1-205462067;