15-78411289-G-A

Position:

• chr15-78411289-G-A

Variant summary

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

The XR_932506.3(LOC105370912):​n.2935G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,122 control chromosomes in the GnomAD database, including 3,120 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 (3120 hom., cov: 32)
• Consequence: LOC105370912 XR_932506.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

LOC105370912 (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 (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370912	XR_932506.3	n.2935G>A		non_coding_transcript_exon_variant	4/4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28657 AN: 152004 Hom.: 3110 Cov.: 32

Gnomad AFR AF: 0.0999

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.189 AC: 28689 AN: 152122 Hom.: 3120 Cov.: 32 AF XY: 0.191 AC XY: 14208 AN XY: 74380

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.218

Alfa AF: 0.203 Hom.: 6793

Bravo AF: 0.192

Asia WGS AF: 0.256 AC: 890 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	2.3
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4887052; hg19: chr15-78703631;