rs13007575

chr2-173813651-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_923588.3(LOC105373745):n.271A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,282 control chromosomes in the GnomAD database, including 1,084 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 0.11 (1084 hom., cov: 32)
• Consequence: LOC105373745 XR_923588.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.08

Genes affected

LOC105373745 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373745	XR_923588.3	n.271A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17051 AN: 152164 Hom.: 1085 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.112 AC: 17057 AN: 152282 Hom.: 1084 Cov.: 32 AF XY: 0.115 AC XY: 8550 AN XY: 74462

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.0987

Alfa AF: 0.104 Hom.: 652

Bravo AF: 0.111

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
Cadd	Benign	19
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13007575; hg19: chr2-174678379;