11-113482039-G-T

Variant names:

• chr11-113482039-G-T
• rs10891556
• XR_948024.2:n.379-2466C>A

Variant summary

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

The XR_948024.2(LOC105369501):​n.379-2466C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,104 control chromosomes in the GnomAD database, including 3,629 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 0.21 (3629 hom., cov: 33)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908
• Publications: 18 publications found

Genes affected

LOC105369501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369501	XR_948024.2	n.379-2466C>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31561 AN: 151986 Hom.: 3613 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.208 AC: 31616 AN: 152104 Hom.: 3629 Cov.: 33 AF XY: 0.213 AC XY: 15843 AN XY: 74354

African (AFR) AF: 0.196 AC: 8117 AN: 41484

American (AMR) AF: 0.297 AC: 4529 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2288 AN: 5170

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2448 AN: 10570

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11923 AN: 67990

Other (OTH) AF: 0.196 AC: 414 AN: 2116

Alfa AF: 0.173 Hom.: 2734

Bravo AF: 0.213

Asia WGS AF: 0.329 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.64
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs10891556; hg19: chr11-113352761;