rs4735765

Variant names:

• chr8-77185569-A-T
• rs4735765
• ENST00000763062.1:n.147-2795A>T

Variant summary

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

The ENST00000763062.1(ENSG00000299381):​n.147-2795A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151,866 control chromosomes in the GnomAD database, including 13,197 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 0.40 (13197 hom., cov: 31)
• Consequence: ENSG00000299381 ENST00000763062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 1 publications found

Genes affected

ENSG00000299381 (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 = 0.541 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
ENSG00000299381	ENST00000763062.1	n.147-2795A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61142 AN: 151744 Hom.: 13148 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.403 AC: 61246 AN: 151866 Hom.: 13197 Cov.: 31 AF XY: 0.404 AC XY: 29985 AN XY: 74200

African (AFR) AF: 0.547 AC: 22636 AN: 41418

American (AMR) AF: 0.381 AC: 5793 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1129 AN: 3466

East Asian (EAS) AF: 0.452 AC: 2322 AN: 5140

South Asian (SAS) AF: 0.472 AC: 2276 AN: 4824

European-Finnish (FIN) AF: 0.263 AC: 2777 AN: 10568

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

European-Non Finnish (NFE) AF: 0.337 AC: 22912 AN: 67942

Other (OTH) AF: 0.400 AC: 840 AN: 2102

Alfa AF: 0.371 Hom.: 1402

Bravo AF: 0.415

Asia WGS AF: 0.480 AC: 1670 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	4.8
DANN	Benign	0.61
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4735765; hg19: chr8-78097805;