rs7168353

Positions:

• chr15-93095172-G-C
• chr15-93095172-G-T

Variant summary

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

The XR_007064769.1(LOC101927025):​n.64+5895G>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 0.191 in 152,144 control chromosomes in the GnomAD database, including 2,950 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 (2950 hom., cov: 32)
• Consequence: LOC101927025 XR_007064769.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

LOC101927025 (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 (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101927025	XR_007064769.1	n.64+5895G>C		intron_variant, non_coding_transcript_variant
LOC101927025	XR_243235.4	n.75+5683G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000711606.1	n.87+5683G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29007 AN: 152026 Hom.: 2946 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.191 AC: 29005 AN: 152144 Hom.: 2950 Cov.: 32 AF XY: 0.188 AC XY: 14001 AN XY: 74380

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.209

Alfa AF: 0.196 Hom.: 1744

Bravo AF: 0.181

Asia WGS AF: 0.200 AC: 698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7168353; hg19: chr15-93638401;