rs17404622

Variant names:

• chr5-31381223-T-C
• rs17404622

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 0.286 in 152,066 control chromosomes in the GnomAD database, including 6,997 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 0.29 (6997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.359 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: 0.286 AC: 43507 AN: 151950 Hom.: 6993 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.286 AC: 43515 AN: 152066 Hom.: 6997 Cov.: 32 AF XY: 0.282 AC XY: 20999 AN XY: 74368

African (AFR) AF: 0.150 AC: 6235 AN: 41480

American (AMR) AF: 0.322 AC: 4927 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3466

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5170

South Asian (SAS) AF: 0.368 AC: 1774 AN: 4822

European-Finnish (FIN) AF: 0.249 AC: 2630 AN: 10572

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.362 AC: 24629 AN: 67962

Other (OTH) AF: 0.315 AC: 666 AN: 2112

Alfa AF: 0.340 Hom.: 5074

Bravo AF: 0.289

Asia WGS AF: 0.305 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.72
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs17404622; hg19: chr5-31381330;