11-106374741-G-A

Variant names:

• chr11-106374741-G-A
• rs638300
• XR_947985.1:n.101+5485G>A

Variant summary

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

The XR_947985.1(LOC105369474):​n.101+5485G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,004 control chromosomes in the GnomAD database, including 15,579 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 0.38 (15579 hom., cov: 32)
• Consequence: LOC105369474 XR_947985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 3 publications found

Genes affected

LOC105369474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57436 AN: 151886 Hom.: 15520 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.379 AC: 57549 AN: 152004 Hom.: 15579 Cov.: 32 AF XY: 0.371 AC XY: 27555 AN XY: 74308

African (AFR) AF: 0.772 AC: 32000 AN: 41470

American (AMR) AF: 0.272 AC: 4149 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3468

East Asian (EAS) AF: 0.113 AC: 584 AN: 5172

South Asian (SAS) AF: 0.202 AC: 972 AN: 4816

European-Finnish (FIN) AF: 0.213 AC: 2253 AN: 10558

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15309 AN: 67946

Other (OTH) AF: 0.387 AC: 813 AN: 2102

Alfa AF: 0.291 Hom.: 9768

Bravo AF: 0.401

Asia WGS AF: 0.242 AC: 844 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs638300; hg19: chr11-106245468;