11-2073073-C-T

Variant names:

• chr11-2073073-C-T
• rs7107076
• ENST00000796724.1:n.322-14475C>T

Variant summary

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

The ENST00000796724.1(ENSG00000303720):​n.322-14475C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,080 control chromosomes in the GnomAD database, including 5,851 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 0.28 (5851 hom., cov: 32)
• Consequence: ENSG00000303720 ENST00000796724.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 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.322-14475C>T		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796725.1	n.299-14472C>T		intron_variant	Intron 2 of 3
ENSG00000303720	ENST00000796726.1	n.299-14475C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41876 AN: 151960 Hom.: 5846 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.276 AC: 41925 AN: 152080 Hom.: 5851 Cov.: 32 AF XY: 0.270 AC XY: 20067 AN XY: 74320

African (AFR) AF: 0.341 AC: 14143 AN: 41464

American (AMR) AF: 0.226 AC: 3464 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3464

East Asian (EAS) AF: 0.260 AC: 1339 AN: 5142

South Asian (SAS) AF: 0.195 AC: 936 AN: 4812

European-Finnish (FIN) AF: 0.216 AC: 2292 AN: 10610

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17531 AN: 67970

Other (OTH) AF: 0.281 AC: 593 AN: 2110

Alfa AF: 0.136 Hom.: 223

Bravo AF: 0.282

Asia WGS AF: 0.249 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.94
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7107076; hg19: chr11-2094303;