chr1-89392631-C-A

Variant names:

• chr1-89392631-C-A
• rs4658149

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 0.203 in 152,022 control chromosomes in the GnomAD database, including 3,931 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 0.20 (3931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.314 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: 0.203 AC: 30910 AN: 151904 Hom.: 3927 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.203 AC: 30915 AN: 152022 Hom.: 3931 Cov.: 32 AF XY: 0.201 AC XY: 14956 AN XY: 74288

African (AFR) AF: 0.0631 AC: 2619 AN: 41500

American (AMR) AF: 0.322 AC: 4910 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3472

East Asian (EAS) AF: 0.0206 AC: 107 AN: 5186

South Asian (SAS) AF: 0.189 AC: 912 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2118 AN: 10534

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18672 AN: 67936

Other (OTH) AF: 0.213 AC: 450 AN: 2108

Alfa AF: 0.245 Hom.: 9716

Bravo AF: 0.207

Asia WGS AF: 0.0990 AC: 345 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4658149; hg19: chr1-89858190; COSMIC: COSV68969218;