rs17728338

Variant names:

• chr5-151098757-G-A
• rs17728338

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 0.0722 in 152,206 control chromosomes in the GnomAD database, including 419 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 0.072 (419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 78 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 = 0.129 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: 0.0722 AC: 10986 AN: 152088 Hom.: 419 Cov.: 32

Gnomad AFR AF: 0.0918

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0646

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0591

Gnomad OTH AF: 0.0818

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

GnomAD4 genome AF: 0.0722 AC: 10986 AN: 152206 Hom.: 419 Cov.: 32 AF XY: 0.0736 AC XY: 5476 AN XY: 74402

African (AFR) AF: 0.0916 AC: 3806 AN: 41538

American (AMR) AF: 0.0459 AC: 702 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 298 AN: 3470

East Asian (EAS) AF: 0.111 AC: 573 AN: 5180

South Asian (SAS) AF: 0.138 AC: 666 AN: 4822

European-Finnish (FIN) AF: 0.0646 AC: 684 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0591 AC: 4017 AN: 68014

Other (OTH) AF: 0.0843 AC: 178 AN: 2112

Alfa AF: 0.0632 Hom.: 1307

Bravo AF: 0.0697

Asia WGS AF: 0.205 AC: 711 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	1.1
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17728338; hg19: chr5-150478318;