rs12346541

Variant names:

• chr9-100718105-G-A
• rs12346541

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 0.216 in 152,192 control chromosomes in the GnomAD database, including 3,954 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 0.22 (3954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.216 AC: 32822 AN: 152074 Hom.: 3947 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.216 AC: 32862 AN: 152192 Hom.: 3954 Cov.: 32 AF XY: 0.220 AC XY: 16362 AN XY: 74404

African (AFR) AF: 0.194 AC: 8068 AN: 41512

American (AMR) AF: 0.381 AC: 5832 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 973 AN: 3470

East Asian (EAS) AF: 0.333 AC: 1717 AN: 5162

South Asian (SAS) AF: 0.149 AC: 719 AN: 4826

European-Finnish (FIN) AF: 0.196 AC: 2082 AN: 10602

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12742 AN: 68014

Other (OTH) AF: 0.237 AC: 501 AN: 2112

Alfa AF: 0.199 Hom.: 13735

Bravo AF: 0.237

Asia WGS AF: 0.219 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.21
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs12346541; hg19: chr9-103480387;