chr1-151910380-C-G

Variant names:

• chr1-151910380-C-G
• rs10788817

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 0.582 in 152,012 control chromosomes in the GnomAD database, including 26,080 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 0.58 (26080 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 24 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 (AMR) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88432 AN: 151894 Hom.: 26061 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.582 AC: 88491 AN: 152012 Hom.: 26080 Cov.: 31 AF XY: 0.582 AC XY: 43242 AN XY: 74318

African (AFR) AF: 0.546 AC: 22627 AN: 41454

American (AMR) AF: 0.671 AC: 10251 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3306 AN: 5162

South Asian (SAS) AF: 0.371 AC: 1787 AN: 4820

European-Finnish (FIN) AF: 0.636 AC: 6731 AN: 10580

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40618 AN: 67952

Other (OTH) AF: 0.587 AC: 1236 AN: 2106

Alfa AF: 0.469 Hom.: 1280

Bravo AF: 0.588

Asia WGS AF: 0.503 AC: 1752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10788817; hg19: chr1-151882856; COSMIC: COSV64295743;