rs9493100

Variant names:

• chr6-131793941-C-T
• rs9493100

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 0.122 in 151,294 control chromosomes in the GnomAD database, including 2,247 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 0.12 (2247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.122 AC: 18399 AN: 151178 Hom.: 2238 Cov.: 31

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.0654

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.122 AC: 18423 AN: 151294 Hom.: 2247 Cov.: 31 AF XY: 0.128 AC XY: 9450 AN XY: 73920

African (AFR) AF: 0.0490 AC: 2024 AN: 41288

American (AMR) AF: 0.282 AC: 4252 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 307 AN: 3446

East Asian (EAS) AF: 0.435 AC: 2241 AN: 5154

South Asian (SAS) AF: 0.207 AC: 998 AN: 4816

European-Finnish (FIN) AF: 0.0847 AC: 891 AN: 10516

Middle Eastern (MID) AF: 0.0634 AC: 18 AN: 284

European-Non Finnish (NFE) AF: 0.106 AC: 7193 AN: 67710

Other (OTH) AF: 0.127 AC: 267 AN: 2100

Alfa AF: 0.114 Hom.: 1669

Bravo AF: 0.133

Asia WGS AF: 0.295 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.46
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9493100; hg19: chr6-132115081; COSMIC: COSV74123801;