rs4779984

Positions:

• chr15-32222725-A-G

Variant summary

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

The XR_007064561.1(LOC102724078):​n.527-14527T>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 0.132 in 151,264 control chromosomes in the GnomAD database, including 1,767 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 0.13 (1767 hom., cov: 30)
• Consequence: LOC102724078 XR_007064561.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

Genes affected

LOC102724078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724078	XR_007064561.1	n.527-14527T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19934 AN: 151154 Hom.: 1765 Cov.: 30

Gnomad AFR AF: 0.0763

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.132 AC: 19954 AN: 151264 Hom.: 1767 Cov.: 30 AF XY: 0.138 AC XY: 10187 AN XY: 73832

Gnomad4 AFR AF: 0.0766

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.128

Alfa AF: 0.135 Hom.: 1130

Bravo AF: 0.131

Asia WGS AF: 0.240 AC: 826 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4779984; hg19: chr15-32514926;