chr2-179348942-T-C

Variant names:

• chr2-179348942-T-C
• rs10186547

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 0.477 in 152,154 control chromosomes in the GnomAD database, including 21,036 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 0.48 (21036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) 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: 0.477 AC: 72479 AN: 152036 Hom.: 21016 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72516 AN: 152154 Hom.: 21036 Cov.: 32 AF XY: 0.487 AC XY: 36192 AN XY: 74380

African (AFR) AF: 0.126 AC: 5247 AN: 41556

American (AMR) AF: 0.622 AC: 9504 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3470

East Asian (EAS) AF: 0.700 AC: 3620 AN: 5170

South Asian (SAS) AF: 0.631 AC: 3045 AN: 4822

European-Finnish (FIN) AF: 0.666 AC: 7047 AN: 10580

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.587 AC: 39906 AN: 67964

Other (OTH) AF: 0.516 AC: 1089 AN: 2110

Alfa AF: 0.552 Hom.: 5080

Bravo AF: 0.460

Asia WGS AF: 0.631 AC: 2194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.80
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs10186547; hg19: chr2-180213669;