chr1-239091110-A-G

Variant names:

• chr1-239091110-A-G
• rs2883160

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 0.299 in 151,864 control chromosomes in the GnomAD database, including 7,446 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 0.30 (7446 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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: 0.299 AC: 45382 AN: 151746 Hom.: 7411 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45460 AN: 151864 Hom.: 7446 Cov.: 31 AF XY: 0.302 AC XY: 22445 AN XY: 74200

African (AFR) AF: 0.395 AC: 16340 AN: 41416

American (AMR) AF: 0.410 AC: 6248 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1024 AN: 3464

East Asian (EAS) AF: 0.217 AC: 1117 AN: 5144

South Asian (SAS) AF: 0.313 AC: 1506 AN: 4804

European-Finnish (FIN) AF: 0.239 AC: 2516 AN: 10538

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15716 AN: 67944

Other (OTH) AF: 0.292 AC: 615 AN: 2104

Alfa AF: 0.286 Hom.: 970

Bravo AF: 0.320

Asia WGS AF: 0.301 AC: 1048 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2883160; hg19: chr1-239254410; COSMIC: COSV60043633;