ENST00000803880.1:n.430-1287A>C

Variant names:

• chr5-73981078-A-C
• rs6894385
• ENST00000803880.1:n.430-1287A>C

Variant summary

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

The ENST00000803880.1(ENSG00000304504):​n.430-1287A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,082 control chromosomes in the GnomAD database, including 2,036 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 0.16 (2036 hom., cov: 32)
• Consequence: ENSG00000304504 ENST00000803880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 7 publications found

Genes affected

ENSG00000304504 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803880.1. 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
	ENSG00000304504	ENST00000803880.1		n.430-1287A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23974 AN: 151964 Hom.: 2035 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.158 AC: 23976 AN: 152082 Hom.: 2036 Cov.: 32 AF XY: 0.156 AC XY: 11618 AN XY: 74338

African (AFR) AF: 0.109 AC: 4520 AN: 41478

American (AMR) AF: 0.122 AC: 1868 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 449 AN: 3460

East Asian (EAS) AF: 0.275 AC: 1413 AN: 5146

South Asian (SAS) AF: 0.274 AC: 1320 AN: 4818

European-Finnish (FIN) AF: 0.144 AC: 1526 AN: 10590

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12336 AN: 67984

Other (OTH) AF: 0.151 AC: 320 AN: 2116

Alfa AF: 0.174 Hom.: 4911

Bravo AF: 0.152

Asia WGS AF: 0.241 AC: 837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6894385; hg19: chr5-73276903;