rs41416652

chr17-34258842-T-C

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 0.0621 in 152,238 control chromosomes in the GnomAD database, including 811 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 0.062 (811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.0621 AC: 9448 AN: 152120 Hom.: 804 Cov.: 32

Gnomad AFR AF: 0.0117

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.0987

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0431

Gnomad OTH AF: 0.0501

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

GnomAD4 genome AF: 0.0621 AC: 9459 AN: 152238 Hom.: 811 Cov.: 32 AF XY: 0.0680 AC XY: 5058 AN XY: 74424

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.0995

Gnomad4 FIN AF: 0.0987

Gnomad4 NFE AF: 0.0431

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0538 Hom.: 82

Bravo AF: 0.0663

Asia WGS AF: 0.260 AC: 901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.4
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41416652; hg19: chr17-32585861;