rs10517731

Variant names:

• chr4-161080078-G-C
• rs10517731
• XR_939408.1:n.144-11985C>G

Variant summary

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

The XR_939408.1(LOC105377514):​n.144-11985C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 151,838 control chromosomes in the GnomAD database, including 739 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 (739 hom., cov: 32)
• Consequence: LOC105377514 XR_939408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430
• Publications: 1 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 = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377514	XR_939408.1	n.144-11985C>G		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12760 AN: 151720 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0586

Gnomad FIN AF: 0.129

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: 0.0840 AC: 12757 AN: 151838 Hom.: 739 Cov.: 32 AF XY: 0.0833 AC XY: 6178 AN XY: 74190

African (AFR) AF: 0.0200 AC: 830 AN: 41490

American (AMR) AF: 0.0798 AC: 1211 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3464

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5158

South Asian (SAS) AF: 0.0594 AC: 287 AN: 4828

European-Finnish (FIN) AF: 0.129 AC: 1361 AN: 10564

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

European-Non Finnish (NFE) AF: 0.123 AC: 8337 AN: 67844

Other (OTH) AF: 0.106 AC: 222 AN: 2102

Alfa AF: 0.101 Hom.: 102

Bravo AF: 0.0804

Asia WGS AF: 0.0360 AC: 124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.36
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10517731; hg19: chr4-162001230;