rs9954571

Variant names:

• chr18-60192644-G-A
• rs9954571

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 0.14 in 152,216 control chromosomes in the GnomAD database, including 1,736 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 0.14 (1736 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.202 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: 0.140 AC: 21276 AN: 152098 Hom.: 1737 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0697

Gnomad EAS AF: 0.0228

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.140 AC: 21285 AN: 152216 Hom.: 1736 Cov.: 32 AF XY: 0.140 AC XY: 10416 AN XY: 74422

African (AFR) AF: 0.206 AC: 8541 AN: 41510

American (AMR) AF: 0.103 AC: 1583 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0697 AC: 242 AN: 3470

East Asian (EAS) AF: 0.0229 AC: 119 AN: 5196

South Asian (SAS) AF: 0.105 AC: 508 AN: 4822

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10596

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8200 AN: 68002

Other (OTH) AF: 0.132 AC: 278 AN: 2114

Alfa AF: 0.126 Hom.: 2661

Bravo AF: 0.136

Asia WGS AF: 0.0790 AC: 275 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	0.35
DANN	Benign	0.76
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9954571; hg19: chr18-57859877;