rs7977406

chr12-114921619-G-Achr12-114921619-G-T

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 0.315 in 151,956 control chromosomes in the GnomAD database, including 7,972 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 0.32 (7972 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47833 AN: 151838 Hom.: 7955 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.315 AC: 47884 AN: 151956 Hom.: 7972 Cov.: 32 AF XY: 0.309 AC XY: 22977 AN XY: 74254

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.328

Alfa AF: 0.261 Hom.: 1702

Bravo AF: 0.320

Asia WGS AF: 0.250 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7977406; hg19: chr12-115359424;