1-191189965-G-C

Variant names:

• chr1-191189965-G-C
• rs1377924

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 0.482 in 151,840 control chromosomes in the GnomAD database, including 17,715 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 0.48 (17715 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73048 AN: 151722 Hom.: 17701 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.482 AC: 73117 AN: 151840 Hom.: 17715 Cov.: 31 AF XY: 0.482 AC XY: 35742 AN XY: 74192

African (AFR) AF: 0.501 AC: 20733 AN: 41422

American (AMR) AF: 0.524 AC: 7995 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1920 AN: 5156

South Asian (SAS) AF: 0.420 AC: 2022 AN: 4810

European-Finnish (FIN) AF: 0.463 AC: 4882 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32235 AN: 67874

Other (OTH) AF: 0.471 AC: 994 AN: 2110

Alfa AF: 0.345 Hom.: 875

Bravo AF: 0.485

Asia WGS AF: 0.435 AC: 1512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.7
DANN	Benign	0.43
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1377924; hg19: chr1-191159095;