chr15-93156598-A-G

Position:

• chr15-93156598-A-G

Variant summary

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

The XR_007064769.1(LOC101927025):​n.398-13845A>G 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 0.198 in 152,136 control chromosomes in the GnomAD database, including 3,098 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 0.20 (3098 hom., cov: 32)
• Consequence: LOC101927025 XR_007064769.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.573

Genes affected

LOC101927025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927025	XR_007064769.1	n.398-13845A>G		intron_variant, non_coding_transcript_variant
LOC101927025	XR_243235.4	n.501-13845A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000711606.1	n.513-13845A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30098 AN: 152016 Hom.: 3099 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.198 AC: 30114 AN: 152136 Hom.: 3098 Cov.: 32 AF XY: 0.199 AC XY: 14820 AN XY: 74384

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.172

Alfa AF: 0.197 Hom.: 5761

Bravo AF: 0.193

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9302364; hg19: chr15-93699827;