2-176072106-A-G

Variant names:

• chr2-176072106-A-G
• rs847126

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 0.393 in 152,094 control chromosomes in the GnomAD database, including 15,126 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 (15126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.71 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: 0.393 AC: 59696 AN: 151976 Hom.: 15092 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.393 AC: 59792 AN: 152094 Hom.: 15126 Cov.: 32 AF XY: 0.392 AC XY: 29117 AN XY: 74356

African (AFR) AF: 0.716 AC: 29702 AN: 41458

American (AMR) AF: 0.333 AC: 5089 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3464

East Asian (EAS) AF: 0.199 AC: 1027 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2576 AN: 4812

European-Finnish (FIN) AF: 0.177 AC: 1880 AN: 10610

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17264 AN: 67988

Other (OTH) AF: 0.372 AC: 788 AN: 2116

Alfa AF: 0.301 Hom.: 31368

Bravo AF: 0.413

Asia WGS AF: 0.363 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.22
DANN	Benign	0.33
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs847126; hg19: chr2-176936834;