rs17234657

Variant names:

• chr5-40401407-T-G
• rs17234657

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 0.14 in 152,112 control chromosomes in the GnomAD database, including 1,710 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 0.14 (1710 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.995
• Publications: 72 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.187 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: 0.140 AC: 21231 AN: 151994 Hom.: 1705 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0859

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.140 AC: 21253 AN: 152112 Hom.: 1710 Cov.: 31 AF XY: 0.138 AC XY: 10264 AN XY: 74366

African (AFR) AF: 0.190 AC: 7884 AN: 41492

American (AMR) AF: 0.0857 AC: 1309 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0174 AC: 84 AN: 4824

European-Finnish (FIN) AF: 0.187 AC: 1982 AN: 10574

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9326 AN: 67976

Other (OTH) AF: 0.111 AC: 235 AN: 2108

Alfa AF: 0.128 Hom.: 6357

Bravo AF: 0.133

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs17234657; hg19: chr5-40401509;