ENST00000796724.1:n.321+8690C>T

Variant names:

• chr11-2049340-C-T
• rs7932964
• ENST00000796724.1:n.321+8690C>T

Variant summary

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

The ENST00000796724.1(ENSG00000303720):​n.321+8690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,736 control chromosomes in the GnomAD database, including 8,148 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 (8148 hom., cov: 31)
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 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.321+8690C>T		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796725.1	n.298+8690C>T		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796726.1	n.298+8690C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49085 AN: 151618 Hom.: 8129 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.324 AC: 49157 AN: 151736 Hom.: 8148 Cov.: 31 AF XY: 0.328 AC XY: 24299 AN XY: 74120

African (AFR) AF: 0.370 AC: 15331 AN: 41398

American (AMR) AF: 0.388 AC: 5920 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3466

East Asian (EAS) AF: 0.255 AC: 1312 AN: 5150

South Asian (SAS) AF: 0.316 AC: 1517 AN: 4796

European-Finnish (FIN) AF: 0.332 AC: 3499 AN: 10542

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19245 AN: 67826

Other (OTH) AF: 0.324 AC: 681 AN: 2104

Alfa AF: 0.301 Hom.: 15466

Bravo AF: 0.330

Asia WGS AF: 0.332 AC: 1156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7932964; hg19: chr11-2070570;