rs1376345

Variant names:

• chr12-97637847-C-T
• rs1376345

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 0.0524 in 152,184 control chromosomes in the GnomAD database, including 316 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 0.052 (316 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0902 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: 0.0525 AC: 7978 AN: 152066 Hom.: 317 Cov.: 33

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.0696

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0524 AC: 7975 AN: 152184 Hom.: 316 Cov.: 33 AF XY: 0.0577 AC XY: 4295 AN XY: 74402

Gnomad4 AFR AF: 0.0265

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.0697

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0566 Hom.: 88

Bravo AF: 0.0450

Asia WGS AF: 0.100 AC: 345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376345; hg19: chr12-98031625;