chr6-32619236-C-T

Variant names:

• chr6-32619236-C-T
• rs557011
• ENST00000843605.1:n.*105G>A

Variant summary

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

The ENST00000843605.1(ENSG00000309733):​n.*105G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,850 control chromosomes in the GnomAD database, including 9,738 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 0.35 (9738 hom., cov: 32)
• Consequence: ENSG00000309733 ENST00000843605.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.642
• Publications: 20 publications found

Genes affected

ENSG00000309733 (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 (EAS) allele frequency at 95% confidence interval = 0.522 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
ENSG00000309733	ENST00000843605.1	n.*105G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53614 AN: 151732 Hom.: 9719 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.354 AC: 53685 AN: 151850 Hom.: 9738 Cov.: 32 AF XY: 0.356 AC XY: 26402 AN XY: 74212

African (AFR) AF: 0.325 AC: 13466 AN: 41420

American (AMR) AF: 0.417 AC: 6367 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1360 AN: 3464

East Asian (EAS) AF: 0.539 AC: 2778 AN: 5156

South Asian (SAS) AF: 0.320 AC: 1540 AN: 4812

European-Finnish (FIN) AF: 0.348 AC: 3659 AN: 10528

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.344 AC: 23382 AN: 67898

Other (OTH) AF: 0.365 AC: 770 AN: 2112

Alfa AF: 0.123 Hom.: 164

Bravo AF: 0.359

Asia WGS AF: 0.415 AC: 1449 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	1.3
DANN	Benign	0.34
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs557011; hg19: chr6-32587013;