ENST00000796724.1:n.322-13045C>A

Variant names:

• chr11-2074503-C-A
• rs6578974
• ENST00000796724.1:n.322-13045C>A

Variant summary

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

The ENST00000796724.1(ENSG00000303720):​n.322-13045C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,996 control chromosomes in the GnomAD database, including 3,950 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 0.17 (3950 hom., cov: 31)
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 7 publications found

Genes affected

ENSG00000303720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 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
ENSG00000303720	ENST00000796724.1	n.322-13045C>A		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796725.1	n.299-13042C>A		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796726.1	n.299-13045C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25368 AN: 151878 Hom.: 3937 Cov.: 31

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.167 AC: 25412 AN: 151996 Hom.: 3950 Cov.: 31 AF XY: 0.161 AC XY: 11952 AN XY: 74312

African (AFR) AF: 0.415 AC: 17153 AN: 41376

American (AMR) AF: 0.0811 AC: 1239 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 329 AN: 3468

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5170

South Asian (SAS) AF: 0.0418 AC: 201 AN: 4814

European-Finnish (FIN) AF: 0.0730 AC: 773 AN: 10586

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0792 AC: 5384 AN: 67992

Other (OTH) AF: 0.137 AC: 288 AN: 2106

Alfa AF: 0.0915 Hom.: 1909

Bravo AF: 0.181

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6578974; hg19: chr11-2095733;