12-78243512-A-C

Variant names:

• chr12-78243512-A-C
• rs795957

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 0.977 in 152,266 control chromosomes in the GnomAD database, including 72,714 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 0.98 (72714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.977 AC: 148685 AN: 152148 Hom.: 72662 Cov.: 32

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.983

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.977 AC: 148796 AN: 152266 Hom.: 72714 Cov.: 32 AF XY: 0.979 AC XY: 72844 AN XY: 74434

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.983

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.984

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.984

Alfa AF: 0.983 Hom.: 67661

Bravo AF: 0.975

Asia WGS AF: 0.980 AC: 3409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs795957; hg19: chr12-78637292;