2-176050237-T-C

Variant names:

• chr2-176050237-T-C
• rs847189

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 0.213 in 152,156 control chromosomes in the GnomAD database, including 3,765 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 0.21 (3765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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: 0.213 AC: 32432 AN: 152038 Hom.: 3761 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.213 AC: 32461 AN: 152156 Hom.: 3765 Cov.: 32 AF XY: 0.207 AC XY: 15370 AN XY: 74386

African (AFR) AF: 0.150 AC: 6242 AN: 41532

American (AMR) AF: 0.199 AC: 3048 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3472

East Asian (EAS) AF: 0.0585 AC: 303 AN: 5178

South Asian (SAS) AF: 0.134 AC: 648 AN: 4818

European-Finnish (FIN) AF: 0.194 AC: 2050 AN: 10582

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18890 AN: 67970

Other (OTH) AF: 0.207 AC: 438 AN: 2116

Alfa AF: 0.250 Hom.: 21676

Bravo AF: 0.211

Asia WGS AF: 0.112 AC: 390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs847189; hg19: chr2-176914965;