ENST00000799372.1:n.141+887A>G

Variant names:

• chr8-125448293-A-G
• rs6470355
• ENST00000799372.1:n.141+887A>G

Variant summary

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

The ENST00000799372.1(ENSG00000304067):​n.141+887A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 152,076 control chromosomes in the GnomAD database, including 6,572 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 0.27 (6572 hom., cov: 32)
• Consequence: ENSG00000304067 ENST00000799372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 5 publications found

Genes affected

ENSG00000304067 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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
ENSG00000304067	ENST00000799372.1	n.141+887A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41511 AN: 151958 Hom.: 6551 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.273 AC: 41584 AN: 152076 Hom.: 6572 Cov.: 32 AF XY: 0.274 AC XY: 20350 AN XY: 74350

African (AFR) AF: 0.427 AC: 17697 AN: 41466

American (AMR) AF: 0.335 AC: 5111 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3472

East Asian (EAS) AF: 0.0970 AC: 502 AN: 5176

South Asian (SAS) AF: 0.332 AC: 1598 AN: 4816

European-Finnish (FIN) AF: 0.172 AC: 1822 AN: 10582

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13624 AN: 67976

Other (OTH) AF: 0.230 AC: 485 AN: 2110

Alfa AF: 0.188 Hom.: 646

Bravo AF: 0.287

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.9
DANN	Benign	0.76
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6470355; hg19: chr8-126460535;