XR_007064798.1:n.2249C>T

Variant names:

• chr15-95032851-G-A
• rs1026453
• XR_007064798.1:n.2249C>T

Variant summary

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

The XR_007064798.1(LOC124903581):​n.2249C>T 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 0.192 in 152,082 control chromosomes in the GnomAD database, including 3,550 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 0.19 (3550 hom., cov: 31)
• Consequence: LOC124903581 XR_007064798.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 4 publications found

Genes affected

LOC124903581 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615751.5. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000293024	ENST00000615751.5	TSL:5	n.380+7793G>A		intron	N/A
	ENSG00000293024	ENST00000616940.1	TSL:5	n.35+7793G>A		intron	N/A
	ENSG00000293024	ENST00000621842.4	TSL:5	n.327+7793G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29144 AN: 151964 Hom.: 3549 Cov.: 31

Gnomad AFR AF: 0.0495

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.192 AC: 29147 AN: 152082 Hom.: 3550 Cov.: 31 AF XY: 0.191 AC XY: 14209 AN XY: 74326

African (AFR) AF: 0.0493 AC: 2046 AN: 41524

American (AMR) AF: 0.340 AC: 5195 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 544 AN: 3464

East Asian (EAS) AF: 0.177 AC: 913 AN: 5162

South Asian (SAS) AF: 0.141 AC: 678 AN: 4824

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10566

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16858 AN: 67958

Other (OTH) AF: 0.192 AC: 404 AN: 2106

Alfa AF: 0.234 Hom.: 2615

Bravo AF: 0.197

Asia WGS AF: 0.140 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.33
DANN	Benign	0.57
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1026453; hg19: chr15-95576080;