ENST00000785193.1:n.477-3876T>C

Variant names:

• chr17-70498167-T-C
• rs10512539
• ENST00000785193.1:n.477-3876T>C

Variant summary

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

The ENST00000785193.1(ENSG00000302248):​n.477-3876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,062 control chromosomes in the GnomAD database, including 3,555 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 0.19 (3555 hom., cov: 32)
• Consequence: ENSG00000302248 ENST00000785193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 2 publications found

Genes affected

ENSG00000302248 (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 = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785193.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302248	ENST00000785193.1		n.477-3876T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29581 AN: 151942 Hom.: 3551 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.195 AC: 29592 AN: 152062 Hom.: 3555 Cov.: 32 AF XY: 0.199 AC XY: 14757 AN XY: 74338

African (AFR) AF: 0.124 AC: 5152 AN: 41518

American (AMR) AF: 0.272 AC: 4141 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3464

East Asian (EAS) AF: 0.592 AC: 3057 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4814

European-Finnish (FIN) AF: 0.0959 AC: 1017 AN: 10602

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13095 AN: 67936

Other (OTH) AF: 0.202 AC: 425 AN: 2108

Alfa AF: 0.182 Hom.: 329

Bravo AF: 0.206

Asia WGS AF: 0.437 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10512539; hg19: chr17-68494308;