rs740026

chr17-65565563-G-A

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 0.353 in 152,120 control chromosomes in the GnomAD database, including 11,122 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 0.35 (11122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.353 AC: 53725 AN: 152002 Hom.: 11121 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.353 AC: 53729 AN: 152120 Hom.: 11122 Cov.: 33 AF XY: 0.354 AC XY: 26325 AN XY: 74352

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.340

Alfa AF: 0.421 Hom.: 7679

Bravo AF: 0.345

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	8.3
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs740026; hg19: chr17-63561681;