rs7980716

chr12-92522853-G-A

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 0.587 in 152,064 control chromosomes in the GnomAD database, including 26,556 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 0.59 (26556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382

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 = 0.663 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: 0.587 AC: 89169 AN: 151946 Hom.: 26528 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.587 AC: 89255 AN: 152064 Hom.: 26556 Cov.: 32 AF XY: 0.586 AC XY: 43512 AN XY: 74308

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.573

Alfa AF: 0.554 Hom.: 47516

Bravo AF: 0.603

Asia WGS AF: 0.607 AC: 2109 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.2
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7980716; hg19: chr12-92916629;