rs1481812

Variant names:

• chr8-71138170-G-A
• rs1481812
• ENST00000647843.1:n.587+16581G>A

Variant summary

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

The ENST00000647843.1(ENSG00000285579):​n.587+16581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0799 in 152,120 control chromosomes in the GnomAD database, including 532 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 0.080 (532 hom., cov: 32)
• Consequence: ENSG00000285579 ENST00000647843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428
• Publications: 1 publications found

Genes affected

ENSG00000285579 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 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
ENSG00000285579	ENST00000647843.1	n.587+16581G>A		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.0799 AC: 12143 AN: 152002 Hom.: 532 Cov.: 32

Gnomad AFR AF: 0.0806

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0550

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0686

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

GnomAD4 genome AF: 0.0799 AC: 12160 AN: 152120 Hom.: 532 Cov.: 32 AF XY: 0.0784 AC XY: 5826 AN XY: 74350

African (AFR) AF: 0.0808 AC: 3352 AN: 41480

American (AMR) AF: 0.0516 AC: 789 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3468

East Asian (EAS) AF: 0.00250 AC: 13 AN: 5194

South Asian (SAS) AF: 0.122 AC: 586 AN: 4810

European-Finnish (FIN) AF: 0.0550 AC: 581 AN: 10572

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0931 AC: 6332 AN: 67996

Other (OTH) AF: 0.0674 AC: 142 AN: 2108

Alfa AF: 0.0868 Hom.: 1043

Bravo AF: 0.0765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.61
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1481812; hg19: chr8-72050405;