rs7172677

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-75132252-A-C
• chr15-75132252-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903530	XR_007064721.1	n.251+1066A>C		intron_variant	Intron 1 of 1

Ensembl

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

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 v4.3

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;