rs1376345

Variant names:

• chr12-97637847-C-T
• rs1376345

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 0.0524 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0265 AC: 1101 AN: 41540

American (AMR) AF: 0.0689 AC: 1052 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.0973 AC: 504 AN: 5182

South Asian (SAS) AF: 0.0697 AC: 336 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1466 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3228 AN: 67986

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0504 Hom.: 331

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1376345; hg19: chr12-98031625;