rs7767301

Variant names:

• chr6-69594590-A-G
• rs7767301
• ENST00000805732.1:n.339-47T>C

Variant summary

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

The ENST00000805732.1(ENSG00000304708):​n.339-47T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 152,306 control chromosomes in the GnomAD database, including 51 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 (51 hom., cov: 32)
• Consequence: ENSG00000304708 ENST00000805732.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 2 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=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0188 (2869/152306) while in subpopulation AFR AF = 0.0431 (1789/41546). AF 95% confidence interval is 0.0414. There are 51 homozygotes in GnomAd4. There are 1409 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 51 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.339-47T>C		intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805733.1	n.522-47T>C		intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805734.1	n.339-47T>C		intron_variant	Intron 2 of 2
ENSG00000304708	ENST00000805735.1	n.96-47T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0188 AC: 2867 AN: 152188 Hom.: 51 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00949

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.0283

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.00207

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00697

Gnomad OTH AF: 0.0144

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

GnomAD4 genome AF: 0.0188 AC: 2869 AN: 152306 Hom.: 51 Cov.: 32 AF XY: 0.0189 AC XY: 1409 AN XY: 74486

African (AFR) AF: 0.0431 AC: 1789 AN: 41546

American (AMR) AF: 0.00948 AC: 145 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0317 AC: 110 AN: 3472

East Asian (EAS) AF: 0.0283 AC: 147 AN: 5188

South Asian (SAS) AF: 0.0302 AC: 146 AN: 4830

European-Finnish (FIN) AF: 0.00207 AC: 22 AN: 10628

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

European-Non Finnish (NFE) AF: 0.00697 AC: 474 AN: 68024

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

Alfa AF: 0.0150 Hom.: 3

Bravo AF: 0.0208

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	-0.92
CADD	Benign	0.48
DANN	Benign	0.43
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs7767301; hg19: chr6-70304482;