rs10503743

Variant names:

• chr8-24106368-A-G
• rs10503743
• XR_001745844.1:n.139-99164A>G

Variant summary

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

The XR_001745844.1(LOC107986931):​n.139-99164A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0922 in 152,076 control chromosomes in the GnomAD database, including 1,626 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 0.092 (1626 hom., cov: 32)
• Consequence: LOC107986931 XR_001745844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 2 publications found

Genes affected

LOC107986931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986931	XR_001745844.1	n.139-99164A>G		intron_variant	Intron 2 of 2
LOC105379328	XR_949589.2	n.*64A>G		downstream_gene_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 13989 AN: 151958 Hom.: 1621 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0938

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0922 AC: 14029 AN: 152076 Hom.: 1626 Cov.: 32 AF XY: 0.0910 AC XY: 6764 AN XY: 74356

African (AFR) AF: 0.269 AC: 11129 AN: 41432

American (AMR) AF: 0.0386 AC: 589 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3470

East Asian (EAS) AF: 0.0935 AC: 481 AN: 5146

South Asian (SAS) AF: 0.0826 AC: 398 AN: 4816

European-Finnish (FIN) AF: 0.0122 AC: 130 AN: 10626

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1009 AN: 67994

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0677 Hom.: 160

Bravo AF: 0.101

Asia WGS AF: 0.123 AC: 425 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs10503743; hg19: chr8-23963881;