chr6-87942862-T-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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;