chr2-171520275-T-C

Variant names:

• chr2-171520275-T-C
• rs3806562

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 0.217 in 152,010 control chromosomes in the GnomAD database, including 4,161 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 0.22 (4161 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 12 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 (AFR) allele frequency at 95% confidence interval = 0.344 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: 0.217 AC: 32956 AN: 151892 Hom.: 4149 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.217 AC: 32997 AN: 152010 Hom.: 4161 Cov.: 32 AF XY: 0.219 AC XY: 16250 AN XY: 74268

African (AFR) AF: 0.349 AC: 14444 AN: 41426

American (AMR) AF: 0.151 AC: 2316 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.142 AC: 733 AN: 5160

South Asian (SAS) AF: 0.160 AC: 772 AN: 4816

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10568

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11090 AN: 67958

Other (OTH) AF: 0.187 AC: 394 AN: 2112

Alfa AF: 0.173 Hom.: 10695

Bravo AF: 0.215

Asia WGS AF: 0.155 AC: 537 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	0.018
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3806562; hg19: chr2-172376785;