17-61418722-T-C

Variant names:

• chr17-61418722-T-C
• rs11868532

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 0.456 in 152,046 control chromosomes in the GnomAD database, including 18,767 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 0.46 (18767 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.457 AC: 69371 AN: 151928 Hom.: 18767 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.456 AC: 69371 AN: 152046 Hom.: 18767 Cov.: 31 AF XY: 0.459 AC XY: 34086 AN XY: 74328

African (AFR) AF: 0.164 AC: 6812 AN: 41500

American (AMR) AF: 0.419 AC: 6410 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2270 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1857 AN: 5160

South Asian (SAS) AF: 0.496 AC: 2382 AN: 4800

European-Finnish (FIN) AF: 0.625 AC: 6611 AN: 10572

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41264 AN: 67944

Other (OTH) AF: 0.484 AC: 1022 AN: 2110

Alfa AF: 0.413 Hom.: 1518

Bravo AF: 0.428

Asia WGS AF: 0.406 AC: 1415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.46
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11868532; hg19: chr17-59496083;