12-61278384-T-G

Variant names:

• chr12-61278384-T-G
• rs7963956

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 0.442 in 151,940 control chromosomes in the GnomAD database, including 15,667 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 0.44 (15667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

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 (AFR) allele frequency at 95% confidence interval = 0.579 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: 0.442 AC: 67075 AN: 151822 Hom.: 15640 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.442 AC: 67157 AN: 151940 Hom.: 15667 Cov.: 32 AF XY: 0.432 AC XY: 32098 AN XY: 74264

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.450

Alfa AF: 0.412 Hom.: 20714

Bravo AF: 0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7963956; hg19: chr12-61672165;