1-151587677-G-C

Variant names:

• chr1-151587677-G-C
• rs1935886

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 0.54 in 152,100 control chromosomes in the GnomAD database, including 24,701 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 0.54 (24701 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.685 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: 0.540 AC: 82123 AN: 151982 Hom.: 24708 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.540 AC: 82142 AN: 152100 Hom.: 24701 Cov.: 33 AF XY: 0.535 AC XY: 39757 AN XY: 74324

African (AFR) AF: 0.274 AC: 11369 AN: 41476

American (AMR) AF: 0.588 AC: 8985 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2357 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1999 AN: 5176

South Asian (SAS) AF: 0.521 AC: 2510 AN: 4822

European-Finnish (FIN) AF: 0.566 AC: 5970 AN: 10552

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46969 AN: 68004

Other (OTH) AF: 0.597 AC: 1260 AN: 2110

Alfa AF: 0.482 Hom.: 1508

Bravo AF: 0.527

Asia WGS AF: 0.478 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.033
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1935886; hg19: chr1-151560153;