rs17172738

Variant names:

• chr7-46640460-C-G
• rs17172738

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 0.413 in 152,044 control chromosomes in the GnomAD database, including 13,880 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 0.41 (13880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.531 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: 0.413 AC: 62791 AN: 151926 Hom.: 13884 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.413 AC: 62805 AN: 152044 Hom.: 13880 Cov.: 32 AF XY: 0.407 AC XY: 30267 AN XY: 74332

African (AFR) AF: 0.269 AC: 11163 AN: 41466

American (AMR) AF: 0.541 AC: 8269 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1614 AN: 3466

East Asian (EAS) AF: 0.457 AC: 2349 AN: 5138

South Asian (SAS) AF: 0.250 AC: 1207 AN: 4826

European-Finnish (FIN) AF: 0.345 AC: 3648 AN: 10582

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32953 AN: 67962

Other (OTH) AF: 0.466 AC: 985 AN: 2114

Alfa AF: 0.435 Hom.: 1834

Bravo AF: 0.428

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.40
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs17172738; hg19: chr7-46680058;