11-113637703-A-G

Variant names:

• chr11-113637703-A-G
• rs1022084
• XR_001748390.2:n.5178+43630T>C

Variant summary

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

The XR_001748390.2(LOC107984390):​n.5178+43630T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,090 control chromosomes in the GnomAD database, including 16,611 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 0.46 (16611 hom., cov: 32)
• Consequence: LOC107984390 XR_001748390.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

LOC107984390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984390	XR_001748390.2	n.5178+43630T>C		intron_variant	Intron 1 of 2
LOC107984390	XR_001748391.2	n.5178+43630T>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70252 AN: 151972 Hom.: 16574 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.463 AC: 70344 AN: 152090 Hom.: 16611 Cov.: 32 AF XY: 0.468 AC XY: 34765 AN XY: 74348

African (AFR) AF: 0.504 AC: 20916 AN: 41510

American (AMR) AF: 0.539 AC: 8234 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3470

East Asian (EAS) AF: 0.661 AC: 3406 AN: 5152

South Asian (SAS) AF: 0.417 AC: 2009 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4832 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28064 AN: 67984

Other (OTH) AF: 0.454 AC: 956 AN: 2104

Alfa AF: 0.344 Hom.: 1129

Bravo AF: 0.478

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.026
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1022084; hg19: chr11-113508425;