chr12-61278384-T-G

Variant names:

• chr12-61278384-T-G
• rs7963956

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 0.442 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.585 AC: 24279 AN: 41482

American (AMR) AF: 0.330 AC: 5020 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1135 AN: 5166

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3256 AN: 10552

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28427 AN: 67916

Other (OTH) AF: 0.450 AC: 950 AN: 2112

Alfa AF: 0.420 Hom.: 48956

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7963956; hg19: chr12-61672165;