11-113493925-G-T

Variant names:

• chr11-113493925-G-T
• rs4245150
• XR_948024.2:n.107-2735C>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.107-2735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 151,994 control chromosomes in the GnomAD database, including 40,019 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 0.72 (40019 hom., cov: 31)
• Consequence: LOC105369501 XR_948024.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 16 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369501	XR_948024.2	n.107-2735C>A		intron_variant	Intron 1 of 5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109114 AN: 151876 Hom.: 39957 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.736

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.719 AC: 109239 AN: 151994 Hom.: 40019 Cov.: 31 AF XY: 0.729 AC XY: 54168 AN XY: 74296

African (AFR) AF: 0.824 AC: 34168 AN: 41466

American (AMR) AF: 0.682 AC: 10415 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3468

East Asian (EAS) AF: 0.974 AC: 5028 AN: 5162

South Asian (SAS) AF: 0.757 AC: 3634 AN: 4802

European-Finnish (FIN) AF: 0.822 AC: 8683 AN: 10558

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43122 AN: 67964

Other (OTH) AF: 0.657 AC: 1384 AN: 2106

Alfa AF: 0.666 Hom.: 56606

Bravo AF: 0.709

Asia WGS AF: 0.867 AC: 3012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4245150; hg19: chr11-113364647;