ENST00000805732.1:n.500G>A

Variant names:

• chr6-69594382-C-T
• rs7747318
• ENST00000805732.1:n.500G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000805732.1(ENSG00000304708):​n.500G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 152,244 control chromosomes in the GnomAD database, including 52 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 0.019 (52 hom., cov: 32)
• Consequence: ENSG00000304708 ENST00000805732.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.822
• Publications: 1 publications found

Genes affected

ENSG00000304708 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0189 (2870/152244) while in subpopulation AFR AF = 0.0431 (1789/41530). AF 95% confidence interval is 0.0414. There are 52 homozygotes in GnomAd4. There are 1410 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 52 gene

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
ENSG00000304708	ENST00000805732.1	n.500G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304708	ENST00000805733.1	n.683G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304708	ENST00000805734.1	n.500G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000304708	ENST00000805735.1	n.257G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2869 AN: 152128 Hom.: 52 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00950

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0307

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00698

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0189 AC: 2870 AN: 152244 Hom.: 52 Cov.: 32 AF XY: 0.0189 AC XY: 1410 AN XY: 74462

African (AFR) AF: 0.0431 AC: 1789 AN: 41530

American (AMR) AF: 0.00948 AC: 145 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3466

East Asian (EAS) AF: 0.0284 AC: 147 AN: 5180

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4824

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10616

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00698 AC: 475 AN: 68022

Other (OTH) AF: 0.0142 AC: 30 AN: 2112

Alfa AF: 0.0146 Hom.: 3

Bravo AF: 0.0207

Asia WGS AF: 0.0290 AC: 103 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	4.5
DANN	Benign	0.66
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs7747318; hg19: chr6-70304274;