chr1-207014862-G-A

Variant names:

• chr1-207014862-G-A
• rs2842721

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 0.377 in 152,028 control chromosomes in the GnomAD database, including 13,832 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 0.38 (13832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 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: 0.377 AC: 57263 AN: 151910 Hom.: 13771 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.377 AC: 57387 AN: 152028 Hom.: 13832 Cov.: 32 AF XY: 0.373 AC XY: 27704 AN XY: 74314

African (AFR) AF: 0.687 AC: 28481 AN: 41436

American (AMR) AF: 0.356 AC: 5446 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1182 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1872 AN: 5174

South Asian (SAS) AF: 0.174 AC: 838 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2258 AN: 10578

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16248 AN: 67962

Other (OTH) AF: 0.391 AC: 825 AN: 2108

Alfa AF: 0.289 Hom.: 13829

Bravo AF: 0.404

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.59
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs2842721; hg19: chr1-207188207;