1-187933850-A-G

Variant names:

• chr1-187933850-A-G
• rs655167

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 0.81 in 152,104 control chromosomes in the GnomAD database, including 51,089 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 0.81 (51089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.810 AC: 123080 AN: 151988 Hom.: 51063 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.810 AC: 123148 AN: 152104 Hom.: 51089 Cov.: 32 AF XY: 0.816 AC XY: 60673 AN XY: 74370

African (AFR) AF: 0.615 AC: 25492 AN: 41426

American (AMR) AF: 0.858 AC: 13093 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2959 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5176 AN: 5180

South Asian (SAS) AF: 0.919 AC: 4437 AN: 4830

European-Finnish (FIN) AF: 0.909 AC: 9644 AN: 10604

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59568 AN: 68012

Other (OTH) AF: 0.817 AC: 1723 AN: 2110

Alfa AF: 0.851 Hom.: 173757

Bravo AF: 0.797

Asia WGS AF: 0.938 AC: 3256 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.79
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs655167; hg19: chr1-187902981;