15-94775998-G-A

Position:

• chr15-94775998-G-A

Variant summary

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

The XR_932644.3(LOC105370988):​n.364-9981C>T 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 0.27 in 152,042 control chromosomes in the GnomAD database, including 6,084 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 0.27 (6084 hom., cov: 33)
• Consequence: LOC105370988 XR_932644.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

LOC105370988 (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 (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370988	XR_932644.3	n.364-9981C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41056 AN: 151924 Hom.: 6088 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.270 AC: 41057 AN: 152042 Hom.: 6084 Cov.: 33 AF XY: 0.268 AC XY: 19893 AN XY: 74332

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.280

Alfa AF: 0.322 Hom.: 7767

Bravo AF: 0.265

Asia WGS AF: 0.326 AC: 1134 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	0.37
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11073388; hg19: chr15-95319227;