chr5-17002976-A-G

Variant names:

• chr5-17002976-A-G
• rs6870564
• ENST00000797284.1:n.460-14480T>C

Variant summary

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

The ENST00000797284.1(ENSG00000303807):​n.460-14480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,792 control chromosomes in the GnomAD database, including 49,836 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 0.80 (49836 hom., cov: 29)
• Consequence: ENSG00000303807 ENST00000797284.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 2 publications found

Genes affected

ENSG00000303807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797284.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303807	ENST00000797284.1		n.460-14480T>C		intron	N/A
	ENSG00000303807	ENST00000797285.1		n.460-14480T>C		intron	N/A
	ENSG00000303807	ENST00000797286.1		n.463-2451T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.804 AC: 121907 AN: 151674 Hom.: 49794 Cov.: 29

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.846

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.804 AC: 122005 AN: 151792 Hom.: 49836 Cov.: 29 AF XY: 0.808 AC XY: 59929 AN XY: 74180

African (AFR) AF: 0.648 AC: 26815 AN: 41358

American (AMR) AF: 0.874 AC: 13296 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4305 AN: 5144

South Asian (SAS) AF: 0.835 AC: 4009 AN: 4804

European-Finnish (FIN) AF: 0.913 AC: 9619 AN: 10534

Middle Eastern (MID) AF: 0.838 AC: 243 AN: 290

European-Non Finnish (NFE) AF: 0.859 AC: 58419 AN: 67970

Other (OTH) AF: 0.827 AC: 1736 AN: 2098

Alfa AF: 0.838 Hom.: 196918

Bravo AF: 0.794

Asia WGS AF: 0.823 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6870564;

hg19: chr5-17003085;