15-40963172-A-T

Position:

• chr15-40963172-A-T

Variant summary

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

The XR_007064601.1(LOC105370789):​n.684A>T 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 0.617 in 151,976 control chromosomes in the GnomAD database, including 29,957 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 0.62 (29957 hom., cov: 32)
• Consequence: LOC105370789 XR_007064601.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

Genes affected

LOC105370789 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370789	XR_007064601.1	n.684A>T		non_coding_transcript_exon_variant	1/4
LOC105370789	XR_001751507.3	n.611A>T		non_coding_transcript_exon_variant	2/4
LOC105370789	XR_932166.4	n.684A>T		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93646 AN: 151858 Hom.: 29925 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.617 AC: 93724 AN: 151976 Hom.: 29957 Cov.: 32 AF XY: 0.617 AC XY: 45804 AN XY: 74268

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.579

Alfa AF: 0.584 Hom.: 3329

Bravo AF: 0.611

Asia WGS AF: 0.602 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4924523; hg19: chr15-41255370;