5-2847579-T-G

Variant names:

• chr5-2847579-T-G
• rs370010
• ENST00000824360.1:n.402-2385T>G

Variant summary

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

The ENST00000824360.1(ENSG00000307167):​n.402-2385T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,826 control chromosomes in the GnomAD database, including 39,519 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 0.72 (39519 hom., cov: 30)
• Consequence: ENSG00000307167 ENST00000824360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 4 publications found

Genes affected

ENSG00000307167 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.781 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
ENSG00000307167	ENST00000824360.1	n.402-2385T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109198 AN: 151708 Hom.: 39487 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.720 AC: 109290 AN: 151826 Hom.: 39519 Cov.: 30 AF XY: 0.717 AC XY: 53230 AN XY: 74220

African (AFR) AF: 0.672 AC: 27792 AN: 41364

American (AMR) AF: 0.793 AC: 12108 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2293 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2775 AN: 5112

South Asian (SAS) AF: 0.682 AC: 3280 AN: 4808

European-Finnish (FIN) AF: 0.728 AC: 7687 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50886 AN: 67942

Other (OTH) AF: 0.712 AC: 1499 AN: 2106

Alfa AF: 0.731 Hom.: 21900

Bravo AF: 0.723

Asia WGS AF: 0.625 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.015
DANN	Benign	0.14
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs370010; hg19: chr5-2847693;