XR_001744246.1:n.1581T>C

Variant names:

• chr6-87942862-T-C
• rs2509458
• XR_001744246.1:n.1581T>C

Variant summary

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

The XR_001744246.1(LOC105377882):​n.1581T>C 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 0.0925 in 152,292 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 0.093 (739 hom., cov: 33)
• Consequence: LOC105377882 XR_001744246.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.88
• Publications: 15 publications found

Genes affected

LOC105377882 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377882	XR_001744246.1	n.1581T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14088 AN: 152174 Hom.: 738 Cov.: 33

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0870

Gnomad FIN AF: 0.0492

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0925 AC: 14092 AN: 152292 Hom.: 739 Cov.: 33 AF XY: 0.0903 AC XY: 6726 AN XY: 74476

African (AFR) AF: 0.0858 AC: 3568 AN: 41564

American (AMR) AF: 0.0826 AC: 1263 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4822

European-Finnish (FIN) AF: 0.0492 AC: 523 AN: 10622

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7343 AN: 68010

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.103 Hom.: 2820

Bravo AF: 0.0946

Asia WGS AF: 0.0680 AC: 238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.49
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2509458; hg19: chr6-88652580;