chr11-13184613-C-A

Variant names:

• chr11-13184613-C-A
• rs748923
• ENST00000741297.1:n.95-3102G>T

Variant summary

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

The ENST00000741297.1(ENSG00000296717):​n.95-3102G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,094 control chromosomes in the GnomAD database, including 2,802 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 (2802 hom., cov: 32)
• Consequence: ENSG00000296717 ENST00000741297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856
• Publications: 3 publications found

Genes affected

ENSG00000296717 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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
ENSG00000296717	ENST00000741297.1	n.95-3102G>T		intron_variant	Intron 1 of 3
ENSG00000296717	ENST00000741299.1	n.80-3102G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25203 AN: 151976 Hom.: 2802 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0922

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0947

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.166 AC: 25226 AN: 152094 Hom.: 2802 Cov.: 32 AF XY: 0.172 AC XY: 12803 AN XY: 74344

African (AFR) AF: 0.277 AC: 11481 AN: 41468

American (AMR) AF: 0.0925 AC: 1414 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2149 AN: 5152

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4820

European-Finnish (FIN) AF: 0.211 AC: 2235 AN: 10572

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0947 AC: 6442 AN: 68002

Other (OTH) AF: 0.120 AC: 253 AN: 2114

Alfa AF: 0.113 Hom.: 3988

Bravo AF: 0.161

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.23
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs748923; hg19: chr11-13206160;