8-78096373-A-G

Variant names:

• chr8-78096373-A-G
• rs1481513
• ENST00000810365.1:n.438-3470A>G

Variant summary

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

The ENST00000810365.1(ENSG00000305312):​n.438-3470A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,754 control chromosomes in the GnomAD database, including 14,963 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 0.44 (14963 hom., cov: 32)
• Consequence: ENSG00000305312 ENST00000810365.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914
• Publications: 3 publications found

Genes affected

ENSG00000305312 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810365.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305312	ENST00000810365.1		n.438-3470A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66055 AN: 151634 Hom.: 14936 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.436 AC: 66126 AN: 151754 Hom.: 14963 Cov.: 32 AF XY: 0.428 AC XY: 31699 AN XY: 74144

African (AFR) AF: 0.524 AC: 21674 AN: 41364

American (AMR) AF: 0.336 AC: 5104 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3468

East Asian (EAS) AF: 0.133 AC: 687 AN: 5170

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4818

European-Finnish (FIN) AF: 0.394 AC: 4146 AN: 10530

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29633 AN: 67888

Other (OTH) AF: 0.432 AC: 911 AN: 2110

Alfa AF: 0.436 Hom.: 47614

Bravo AF: 0.434

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.73
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs1481513; hg19: chr8-79008608;