2-170862736-C-T

Variant names:

• chr2-170862736-C-T
• rs17701824

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 0.376 in 151,950 control chromosomes in the GnomAD database, including 11,532 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 0.38 (11532 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 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: 0.376 AC: 57053 AN: 151832 Hom.: 11529 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.376 AC: 57075 AN: 151950 Hom.: 11532 Cov.: 31 AF XY: 0.379 AC XY: 28151 AN XY: 74250

African (AFR) AF: 0.231 AC: 9569 AN: 41468

American (AMR) AF: 0.334 AC: 5109 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1664 AN: 5162

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4818

European-Finnish (FIN) AF: 0.531 AC: 5576 AN: 10504

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30518 AN: 67932

Other (OTH) AF: 0.378 AC: 795 AN: 2104

Alfa AF: 0.429 Hom.: 7542

Bravo AF: 0.356

Asia WGS AF: 0.359 AC: 1249 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	5.5
DANN	Benign	0.44
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs17701824; hg19: chr2-171719246;