rs7977406

Variant names:

• chr12-114921619-G-A
• rs7977406

Your query was ambiguous. Multiple possible variants found:

• chr12-114921619-G-A
• chr12-114921619-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;