rs12677395

Variant names:

• chr8-115237679-G-A
• rs12677395
• ENST00000748853.1:n.253+24828G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-115237679-G-A
• chr8-115237679-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000748853.1(ENSG00000297548):​n.253+24828G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297548 ENST00000748853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 0 publications found

Genes affected

ENSG00000297548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297548	ENST00000748853.1	n.253+24828G>A		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.0252 AC: 1047 AN: 41478

American (AMR) AF: 0.100 AC: 1530 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5168

South Asian (SAS) AF: 0.101 AC: 489 AN: 4822

European-Finnish (FIN) AF: 0.122 AC: 1282 AN: 10532

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0880 AC: 5983 AN: 67966

Other (OTH) AF: 0.0712 AC: 150 AN: 2108

Alfa AF: 0.0804 Hom.: 87

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs12677395; hg19: chr8-116249908;