rs12677395

chr8-115237679-G-Achr8-115237679-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 0.0808 in 152,014 control chromosomes in the GnomAD database, including 708 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 0.081 (708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 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: 0.0808 AC: 12267 AN: 151896 Hom.: 701 Cov.: 32

Gnomad AFR AF: 0.0253

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0995

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0808 AC: 12288 AN: 152014 Hom.: 708 Cov.: 32 AF XY: 0.0858 AC XY: 6371 AN XY: 74278

Gnomad4 AFR AF: 0.0252

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.0703

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0880

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0812 Hom.: 85

Bravo AF: 0.0763

Asia WGS AF: 0.140 AC: 485 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12677395; hg19: chr8-116249908;