3-78006796-C-T

Variant names:

• chr3-78006796-C-T
• rs7610746
• ENST00000756757.1:n.234+16005G>A

Variant summary

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

The ENST00000756757.1(ENSG00000298601):​n.234+16005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,984 control chromosomes in the GnomAD database, including 7,318 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 0.30 (7318 hom., cov: 32)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 0 publications found

Genes affected

ENSG00000298601 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756757.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298601	ENST00000756757.1		n.234+16005G>A		intron	N/A
	ENSG00000298601	ENST00000756759.1		n.189+16005G>A		intron	N/A
	ENSG00000298601	ENST00000756760.1		n.220+16005G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45799 AN: 151866 Hom.: 7308 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.301 AC: 45821 AN: 151984 Hom.: 7318 Cov.: 32 AF XY: 0.299 AC XY: 22186 AN XY: 74292

African (AFR) AF: 0.230 AC: 9549 AN: 41476

American (AMR) AF: 0.230 AC: 3504 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1136 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2363 AN: 5122

South Asian (SAS) AF: 0.229 AC: 1102 AN: 4822

European-Finnish (FIN) AF: 0.339 AC: 3585 AN: 10568

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23525 AN: 67942

Other (OTH) AF: 0.291 AC: 614 AN: 2110

Alfa AF: 0.310 Hom.: 3902

Bravo AF: 0.294

Asia WGS AF: 0.336 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.47
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs7610746; hg19: chr3-78055947;