15-95585278-G-C

Position:

• chr15-95585278-G-C

Variant summary

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

The XR_932653.1(LOC105370995):​n.139-6692G>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 0.519 in 151,966 control chromosomes in the GnomAD database, including 23,032 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 0.52 (23032 hom., cov: 31)
• Consequence: LOC105370995 XR_932653.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

LOC105370995 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370995	XR_932653.1	n.139-6692G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78721 AN: 151848 Hom.: 22984 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.519 AC: 78824 AN: 151966 Hom.: 23032 Cov.: 31 AF XY: 0.520 AC XY: 38606 AN XY: 74268

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.475

Alfa AF: 0.256 Hom.: 518

Bravo AF: 0.536

Asia WGS AF: 0.554 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2397813; hg19: chr15-96128507;