rs10517733

Variant names:

• chr4-161070588-T-G
• rs10517733
• XR_939408.1:n.144-2495A>C

Variant summary

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

The XR_939408.1(LOC105377514):​n.144-2495A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0838 in 151,110 control chromosomes in the GnomAD database, including 736 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 0.084 (736 hom., cov: 32)
• Consequence: LOC105377514 XR_939408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 5 publications found

Genes affected

LOC105377514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377514	XR_939408.1	n.144-2495A>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12662 AN: 150992 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0199

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0797

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0582

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0838 AC: 12659 AN: 151110 Hom.: 736 Cov.: 32 AF XY: 0.0832 AC XY: 6150 AN XY: 73884

African (AFR) AF: 0.0199 AC: 823 AN: 41446

American (AMR) AF: 0.0796 AC: 1201 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 395 AN: 3446

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5150

South Asian (SAS) AF: 0.0591 AC: 285 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10602

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8246 AN: 67248

Other (OTH) AF: 0.105 AC: 221 AN: 2098

Alfa AF: 0.114 Hom.: 1818

Bravo AF: 0.0803

Asia WGS AF: 0.0350 AC: 121 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs10517733; hg19: chr4-161991740;