rs9965173

Positions:

• chr18-7211757-A-G
• chr18-7211757-A-T

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 0.103 in 152,292 control chromosomes in the GnomAD database, including 1,049 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 0.10 (1049 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15707 AN: 152174 Hom.: 1045 Cov.: 33

Gnomad AFR AF: 0.0537

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.0869

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.103 AC: 15723 AN: 152292 Hom.: 1049 Cov.: 33 AF XY: 0.106 AC XY: 7910 AN XY: 74482

Gnomad4 AFR AF: 0.0537

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.0869

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.105

Alfa AF: 0.113 Hom.: 1013

Bravo AF: 0.107

Asia WGS AF: 0.194 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9965173; hg19: chr18-7211755;