11-34754784-C-T

Variant names:

• chr11-34754784-C-T
• rs7924717
• ENST00000843048.1:n.656+177C>T

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.656+177C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,100 control chromosomes in the GnomAD database, including 3,428 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 0.19 (3428 hom., cov: 32)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 2 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1044+177C>T		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309692	ENST00000843048.1	n.656+177C>T		intron_variant	Intron 2 of 2
ENSG00000309692	ENST00000843049.1	n.848+177C>T		intron_variant	Intron 3 of 3
ENSG00000309692	ENST00000843050.1	n.440+177C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28182 AN: 151982 Hom.: 3416 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.186 AC: 28228 AN: 152100 Hom.: 3428 Cov.: 32 AF XY: 0.192 AC XY: 14313 AN XY: 74362

African (AFR) AF: 0.304 AC: 12615 AN: 41456

American (AMR) AF: 0.146 AC: 2226 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 234 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2210 AN: 5176

South Asian (SAS) AF: 0.269 AC: 1295 AN: 4812

European-Finnish (FIN) AF: 0.192 AC: 2027 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7241 AN: 68000

Other (OTH) AF: 0.155 AC: 326 AN: 2110

Alfa AF: 0.127 Hom.: 4832

Bravo AF: 0.185

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs7924717; hg19: chr11-34776331;