ENST00000810475.1:n.94-13573C>A

Variant names:

• chr6-24106865-C-A
• rs6922632
• ENST00000810475.1:n.94-13573C>A

Variant summary

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

The ENST00000810475.1(ENSG00000305332):​n.94-13573C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,108 control chromosomes in the GnomAD database, including 2,713 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 0.17 (2713 hom., cov: 32)
• Consequence: ENSG00000305332 ENST00000810475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 8 publications found

Genes affected

ENSG00000305332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 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
ENSG00000305332	ENST00000810475.1	n.94-13573C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26178 AN: 151990 Hom.: 2710 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.0637

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.172 AC: 26193 AN: 152108 Hom.: 2713 Cov.: 32 AF XY: 0.165 AC XY: 12304 AN XY: 74356

African (AFR) AF: 0.286 AC: 11848 AN: 41456

American (AMR) AF: 0.125 AC: 1908 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3470

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5186

South Asian (SAS) AF: 0.0643 AC: 309 AN: 4802

European-Finnish (FIN) AF: 0.0883 AC: 935 AN: 10590

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10172 AN: 68008

Other (OTH) AF: 0.165 AC: 349 AN: 2110

Alfa AF: 0.151 Hom.: 8425

Bravo AF: 0.181

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.54
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs6922632; hg19: chr6-24107093;