rs1936473

Variant names:

• chr9-88699926-C-T
• rs1936473

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 0.49 in 152,040 control chromosomes in the GnomAD database, including 19,279 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 0.49 (19279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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: 0.491 AC: 74544 AN: 151920 Hom.: 19281 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.490 AC: 74564 AN: 152040 Hom.: 19279 Cov.: 32 AF XY: 0.487 AC XY: 36166 AN XY: 74314

African (AFR) AF: 0.345 AC: 14296 AN: 41488

American (AMR) AF: 0.438 AC: 6688 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1506 AN: 5162

South Asian (SAS) AF: 0.548 AC: 2635 AN: 4806

European-Finnish (FIN) AF: 0.556 AC: 5862 AN: 10546

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39894 AN: 67974

Other (OTH) AF: 0.510 AC: 1079 AN: 2114

Alfa AF: 0.524 Hom.: 3021

Bravo AF: 0.473

Asia WGS AF: 0.395 AC: 1371 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	0.11
DANN	Benign	0.65
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1936473; hg19: chr9-91314841;