rs17697518

Variant names:

• chr18-41185695-C-T
• rs17697518

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 0.0944 in 152,134 control chromosomes in the GnomAD database, including 827 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 0.094 (827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.0945 AC: 14360 AN: 152018 Hom.: 826 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.0591

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.0944 AC: 14361 AN: 152134 Hom.: 827 Cov.: 32 AF XY: 0.0945 AC XY: 7024 AN XY: 74366

African (AFR) AF: 0.0330 AC: 1371 AN: 41518

American (AMR) AF: 0.0859 AC: 1312 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3464

East Asian (EAS) AF: 0.0591 AC: 306 AN: 5180

South Asian (SAS) AF: 0.122 AC: 585 AN: 4812

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10570

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8546 AN: 68002

Other (OTH) AF: 0.0968 AC: 204 AN: 2108

Alfa AF: 0.109 Hom.: 1338

Bravo AF: 0.0865

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs17697518; hg19: chr18-38765659;