rs10517733

chr4-161070588-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_939408.1(LOC105377514):n.144-2495A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

Genes affected

LOC105377514 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377514	XR_939408.1	n.144-2495A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0199

Gnomad4 AMR AF: 0.0796

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0591

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.105

Alfa AF: 0.117 Hom.: 1371

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517733; hg19: chr4-161991740;