chr8-24106368-A-G

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;