rs7359623

Positions:

• chr17-39893336-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.441 in 152,022 control chromosomes in the GnomAD database, including 15,199 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 0.44 (15199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66991 AN: 151904 Hom.: 15180 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.441 AC: 67059 AN: 152022 Hom.: 15199 Cov.: 32 AF XY: 0.443 AC XY: 32891 AN XY: 74290

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.425

Alfa AF: 0.437 Hom.: 2931

Bravo AF: 0.419

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7359623; hg19: chr17-38049589;