12-61563638-A-G

Variant names:

• chr12-61563638-A-G
• rs7296490

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 0.447 in 151,774 control chromosomes in the GnomAD database, including 16,104 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 0.45 (16104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.526 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: 0.447 AC: 67779 AN: 151656 Hom.: 16105 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.447 AC: 67794 AN: 151774 Hom.: 16104 Cov.: 32 AF XY: 0.446 AC XY: 33058 AN XY: 74158

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.478

Alfa AF: 0.523 Hom.: 27535

Bravo AF: 0.444

Asia WGS AF: 0.415 AC: 1441 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7296490; hg19: chr12-61957419;