rs12377498

Variant names:

• chr9-35150844-C-T
• rs12377498

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0100

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.325

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12377498; hg19: chr9-35150841;