17-27741716-G-A

Variant names:

• chr17-27741716-G-A
• rs953527

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 0.469 in 152,068 control chromosomes in the GnomAD database, including 16,993 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 0.47 (16993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.469 AC: 71298 AN: 151950 Hom.: 16980 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.469 AC: 71343 AN: 152068 Hom.: 16993 Cov.: 33 AF XY: 0.468 AC XY: 34820 AN XY: 74340

African (AFR) AF: 0.525 AC: 21781 AN: 41482

American (AMR) AF: 0.501 AC: 7651 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1612 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2513 AN: 5168

South Asian (SAS) AF: 0.463 AC: 2235 AN: 4828

European-Finnish (FIN) AF: 0.406 AC: 4293 AN: 10566

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29488 AN: 67966

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.450 Hom.: 2014

Bravo AF: 0.479

Asia WGS AF: 0.450 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.023
DANN	Benign	0.79
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs953527; hg19: chr17-26068742;