rs17350440

Variant names:

• chr4-141240325-A-C
• rs17350440

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 0.271 in 152,146 control chromosomes in the GnomAD database, including 6,015 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 0.27 (6015 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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: 0.271 AC: 41174 AN: 152028 Hom.: 6025 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 152146 Hom.: 6015 Cov.: 33 AF XY: 0.272 AC XY: 20227 AN XY: 74372

African (AFR) AF: 0.286 AC: 11871 AN: 41500

American (AMR) AF: 0.256 AC: 3913 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3138 AN: 5162

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4824

European-Finnish (FIN) AF: 0.206 AC: 2187 AN: 10596

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16555 AN: 67996

Other (OTH) AF: 0.279 AC: 588 AN: 2108

Alfa AF: 0.252 Hom.: 2806

Bravo AF: 0.278

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs17350440; hg19: chr4-142161479;