rs7172677

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064721.1(LOC124903530):​n.251+1066A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

LOC124903530 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124903530	XR_007064721.1	n.251+1066A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.758

Alfa AF: 0.728 Hom.: 62469

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7172677; hg19: chr15-75424593;