ENST00000785996.1:n.369+7993T>C

Variant names:

• chr5-68011634-A-G
• rs10067755
• ENST00000785996.1:n.369+7993T>C

Variant summary

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

The ENST00000785996.1(ENSG00000302346):​n.369+7993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,072 control chromosomes in the GnomAD database, including 11,924 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 0.39 (11924 hom., cov: 32)
• Consequence: ENSG00000302346 ENST00000785996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 5 publications found

Genes affected

ENSG00000302346 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785996.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302346	ENST00000785996.1		n.369+7993T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59412 AN: 151954 Hom.: 11908 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.391 AC: 59474 AN: 152072 Hom.: 11924 Cov.: 32 AF XY: 0.391 AC XY: 29093 AN XY: 74328

African (AFR) AF: 0.400 AC: 16608 AN: 41482

American (AMR) AF: 0.451 AC: 6896 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1644 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3146 AN: 5168

South Asian (SAS) AF: 0.298 AC: 1431 AN: 4810

European-Finnish (FIN) AF: 0.307 AC: 3243 AN: 10566

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25088 AN: 67984

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.378 Hom.: 33597

Bravo AF: 0.408

Asia WGS AF: 0.444 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs10067755; hg19: chr5-67307462;