rs12377498

Variant names:

• chr9-35150844-C-T
• rs12377498

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 0.302 in 152,178 control chromosomes in the GnomAD database, including 8,768 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 0.30 (8768 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 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: 0.302 AC: 45967 AN: 152060 Hom.: 8762 Cov.: 32

Gnomad AFR AF: 0.0983

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.00983

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.302 AC: 45973 AN: 152178 Hom.: 8768 Cov.: 32 AF XY: 0.300 AC XY: 22299 AN XY: 74396

African (AFR) AF: 0.0981 AC: 4074 AN: 41548

American (AMR) AF: 0.400 AC: 6116 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3468

East Asian (EAS) AF: 0.0100 AC: 52 AN: 5176

South Asian (SAS) AF: 0.181 AC: 871 AN: 4824

European-Finnish (FIN) AF: 0.461 AC: 4885 AN: 10592

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27612 AN: 67962

Other (OTH) AF: 0.325 AC: 686 AN: 2110

Alfa AF: 0.357 Hom.: 1375

Bravo AF: 0.290

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.48
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12377498; hg19: chr9-35150841;