XR_007059678.1:n.2172T>C

Variant names:

• chr6-90499109-A-G
• rs284515
• XR_007059678.1:n.2172T>C

Variant summary

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

The XR_007059678.1(LOC124901362):​n.2172T>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 0.121 in 152,224 control chromosomes in the GnomAD database, including 1,278 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 (1278 hom., cov: 33)
• Consequence: LOC124901362 XR_007059678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 7 publications found

Genes affected

LOC124901362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18369 AN: 152106 Hom.: 1278 Cov.: 33

Gnomad AFR AF: 0.0725

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.121 AC: 18382 AN: 152224 Hom.: 1278 Cov.: 33 AF XY: 0.124 AC XY: 9243 AN XY: 74424

African (AFR) AF: 0.0726 AC: 3015 AN: 41530

American (AMR) AF: 0.0883 AC: 1351 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 660 AN: 3472

East Asian (EAS) AF: 0.172 AC: 892 AN: 5172

South Asian (SAS) AF: 0.250 AC: 1205 AN: 4826

European-Finnish (FIN) AF: 0.171 AC: 1812 AN: 10596

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8975 AN: 68016

Other (OTH) AF: 0.137 AC: 289 AN: 2114

Alfa AF: 0.133 Hom.: 183

Bravo AF: 0.107

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.44
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs284515; hg19: chr6-91208828;