rs847153

Variant names:

• chr2-176098261-G-A
• rs847153

Your query was ambiguous. Multiple possible variants found:

• chr2-176098261-G-A
• chr2-176098261-G-C
• chr2-176098261-G-T

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 0.39 in 152,126 control chromosomes in the GnomAD database, including 12,939 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 0.39 (12939 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.574 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: 0.390 AC: 59274 AN: 152008 Hom.: 12907 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.0651

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.390 AC: 59358 AN: 152126 Hom.: 12939 Cov.: 33 AF XY: 0.382 AC XY: 28434 AN XY: 74370

African (AFR) AF: 0.580 AC: 24053 AN: 41484

American (AMR) AF: 0.386 AC: 5905 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3472

East Asian (EAS) AF: 0.0647 AC: 334 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1157 AN: 4828

European-Finnish (FIN) AF: 0.296 AC: 3138 AN: 10600

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22718 AN: 67972

Other (OTH) AF: 0.367 AC: 775 AN: 2112

Alfa AF: 0.351 Hom.: 38874

Bravo AF: 0.408

Asia WGS AF: 0.214 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.50
PhyloP100		0.086

Splicing

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

Other links and lift over

dbSNP: rs847153; hg19: chr2-176962989;