rs41416652

Variant names:

• chr17-34258842-T-C
• rs41416652

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 0.0621 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0117 AC: 486 AN: 41562

American (AMR) AF: 0.134 AC: 2054 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.418 AC: 2157 AN: 5160

South Asian (SAS) AF: 0.0995 AC: 480 AN: 4824

European-Finnish (FIN) AF: 0.0987 AC: 1046 AN: 10596

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0431 AC: 2930 AN: 68020

Other (OTH) AF: 0.0520 AC: 110 AN: 2116

Alfa AF: 0.0558 Hom.: 1040

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs41416652; hg19: chr17-32585861;