rs17385675

Variant names:

• chr2-201942473-C-T
• rs17385675

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 0.0613 in 152,146 control chromosomes in the GnomAD database, including 342 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 0.061 (342 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 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: 0.0614 AC: 9332 AN: 152028 Hom.: 343 Cov.: 31

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0753

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0613 AC: 9325 AN: 152146 Hom.: 342 Cov.: 31 AF XY: 0.0595 AC XY: 4429 AN XY: 74388

African (AFR) AF: 0.0282 AC: 1169 AN: 41512

American (AMR) AF: 0.0752 AC: 1149 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5174

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4818

European-Finnish (FIN) AF: 0.0486 AC: 515 AN: 10586

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0820 AC: 5575 AN: 67988

Other (OTH) AF: 0.0781 AC: 165 AN: 2114

Alfa AF: 0.0770 Hom.: 1274

Bravo AF: 0.0625

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0080
DANN	Benign	0.58
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17385675; hg19: chr2-202807196;