rs13020355

Positions:

• chr2-155870662-T-C

Variant summary

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

The XR_007088689.1(LOC105373703):​n.634+35698A>G 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 0.121 in 152,154 control chromosomes in the GnomAD database, including 1,328 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 0.12 (1328 hom., cov: 32)
• Consequence: LOC105373703 XR_007088689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.71

Genes affected

LOC105373703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373703	XR_007088689.1	n.634+35698A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18440 AN: 152036 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.121 AC: 18448 AN: 152154 Hom.: 1328 Cov.: 32 AF XY: 0.123 AC XY: 9141 AN XY: 74400

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.136

Alfa AF: 0.127 Hom.: 655

Bravo AF: 0.116

Asia WGS AF: 0.183 AC: 636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	19
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13020355; hg19: chr2-156727174;