chr2-176205398-G-A

Variant names:

• chr2-176205398-G-A
• rs6749771

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 0.546 in 152,100 control chromosomes in the GnomAD database, including 23,193 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 0.55 (23193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.606 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: 0.546 AC: 82955 AN: 151982 Hom.: 23161 Cov.: 33

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.546 AC: 83023 AN: 152100 Hom.: 23193 Cov.: 33 AF XY: 0.535 AC XY: 39800 AN XY: 74350

African (AFR) AF: 0.517 AC: 21432 AN: 41470

American (AMR) AF: 0.444 AC: 6793 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2337 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1690 AN: 5166

South Asian (SAS) AF: 0.362 AC: 1741 AN: 4810

European-Finnish (FIN) AF: 0.526 AC: 5568 AN: 10580

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41552 AN: 67988

Other (OTH) AF: 0.571 AC: 1207 AN: 2114

Alfa AF: 0.578 Hom.: 13499

Bravo AF: 0.541

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.44
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs6749771; hg19: chr2-177070126;