rs6497031

Positions:

• chr15-93170437-G-A
• chr15-93170437-G-C

Variant summary

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

The XR_007064769.1(LOC101927025):​n.398-6G>A variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,090 control chromosomes in the GnomAD database, including 2,858 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 0.19 (2858 hom., cov: 32)
• Consequence: LOC101927025 XR_007064769.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

Genes affected

LOC101927025 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927025	XR_007064769.1	n.398-6G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
LOC101927025	XR_243235.4	n.501-6G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000711606.1	n.513-6G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28734 AN: 151972 Hom.: 2856 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.189 AC: 28765 AN: 152090 Hom.: 2858 Cov.: 32 AF XY: 0.189 AC XY: 14078 AN XY: 74338

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.173

Alfa AF: 0.149 Hom.: 1102

Bravo AF: 0.195

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6497031; hg19: chr15-93713666;