chr11-24070856-T-C

Variant names:

• chr11-24070856-T-C
• rs2176793
• ENST00000834536.1:n.201-9342A>G

Variant summary

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

The ENST00000834536.1(ENSG00000308482):​n.201-9342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,232 control chromosomes in the GnomAD database, including 615 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 0.056 (615 hom., cov: 32)
• Consequence: ENSG00000308482 ENST00000834536.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 0 publications found

Genes affected

ENSG00000308482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.212 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
ENSG00000308482	ENST00000834536.1	n.201-9342A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8490 AN: 152114 Hom.: 612 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0206

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0563

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0558 AC: 8497 AN: 152232 Hom.: 615 Cov.: 32 AF XY: 0.0576 AC XY: 4288 AN XY: 74418

African (AFR) AF: 0.0123 AC: 509 AN: 41544

American (AMR) AF: 0.218 AC: 3329 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5180

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4824

European-Finnish (FIN) AF: 0.0206 AC: 219 AN: 10620

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3827 AN: 68016

Other (OTH) AF: 0.0464 AC: 98 AN: 2110

Alfa AF: 0.0553 Hom.: 487

Bravo AF: 0.0701

Asia WGS AF: 0.0420 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2176793; hg19: chr11-24092402;