7-35515178-C-T

Variant names:

• chr7-35515178-C-T
• rs343064
• ENST00000806236.1:n.*69G>A

Variant summary

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

The ENST00000806236.1(ENSG00000304779):​n.*69G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,576 control chromosomes in the GnomAD database, including 9,169 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 0.32 (9169 hom., cov: 31)
• Consequence: ENSG00000304779 ENST00000806236.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 12 publications found

Genes affected

ENSG00000304779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 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
ENSG00000304779	ENST00000806236.1	n.*69G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49126 AN: 151458 Hom.: 9156 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.506

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.324 AC: 49161 AN: 151576 Hom.: 9169 Cov.: 31 AF XY: 0.326 AC XY: 24117 AN XY: 74024

African (AFR) AF: 0.141 AC: 5798 AN: 41258

American (AMR) AF: 0.391 AC: 5959 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5160

South Asian (SAS) AF: 0.467 AC: 2244 AN: 4802

European-Finnish (FIN) AF: 0.334 AC: 3476 AN: 10422

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26557 AN: 67928

Other (OTH) AF: 0.340 AC: 718 AN: 2110

Alfa AF: 0.368 Hom.: 18821

Bravo AF: 0.319

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.53
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs343064; hg19: chr7-35554788;