XR_007064721.1:n.251+1066A>C

Variant names:

• chr15-75132252-A-C
• rs7172677
• XR_007064721.1:n.251+1066A>C

Variant summary

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

The XR_007064721.1(LOC124903530):​n.251+1066A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 152,158 control chromosomes in the GnomAD database, including 39,153 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 0.72 (39153 hom., cov: 32)
• Consequence: LOC124903530 XR_007064721.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 17 publications found

Genes affected

LOC124903530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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: 0.716 AC: 108936 AN: 152040 Hom.: 39109 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.717 AC: 109036 AN: 152158 Hom.: 39153 Cov.: 32 AF XY: 0.713 AC XY: 53053 AN XY: 74372

African (AFR) AF: 0.693 AC: 28768 AN: 41504

American (AMR) AF: 0.743 AC: 11370 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2680 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4025 AN: 5176

South Asian (SAS) AF: 0.754 AC: 3637 AN: 4826

European-Finnish (FIN) AF: 0.639 AC: 6753 AN: 10570

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49339 AN: 67996

Other (OTH) AF: 0.758 AC: 1603 AN: 2116

Alfa AF: 0.728 Hom.: 86590

Bravo AF: 0.724

Asia WGS AF: 0.800 AC: 2781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7172677; hg19: chr15-75424593;