rs9381040

Variant names:

• chr6-41186912-C-T
• rs9381040

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 0.289 in 152,070 control chromosomes in the GnomAD database, including 6,516 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 0.29 (6516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 47 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.353 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: 0.289 AC: 43921 AN: 151952 Hom.: 6515 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.289 AC: 43949 AN: 152070 Hom.: 6516 Cov.: 32 AF XY: 0.293 AC XY: 21769 AN XY: 74336

African (AFR) AF: 0.224 AC: 9282 AN: 41478

American (AMR) AF: 0.361 AC: 5512 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5166

South Asian (SAS) AF: 0.338 AC: 1630 AN: 4826

European-Finnish (FIN) AF: 0.312 AC: 3296 AN: 10562

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20458 AN: 67974

Other (OTH) AF: 0.288 AC: 608 AN: 2108

Alfa AF: 0.298 Hom.: 26860

Bravo AF: 0.289

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.053
DANN	Benign	0.62
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9381040; hg19: chr6-41154650;