rs1356951

Variant names:

• chr12-118585496-C-T
• rs1356951

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 0.381 in 152,020 control chromosomes in the GnomAD database, including 11,668 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 0.38 (11668 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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 = 0.429 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: 0.381 AC: 57856 AN: 151902 Hom.: 11664 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.381 AC: 57888 AN: 152020 Hom.: 11668 Cov.: 32 AF XY: 0.375 AC XY: 27869 AN XY: 74302

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.0182

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.397

Alfa AF: 0.403 Hom.: 2097

Bravo AF: 0.371

Asia WGS AF: 0.237 AC: 827 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	3.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1356951; hg19: chr12-119023301;