15-93598604-T-G

Position:

• chr15-93598604-T-G

Variant summary

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

The XR_001751681.2(LOC107983974):​n.1032+5871T>G 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 0.104 in 152,160 control chromosomes in the GnomAD database, including 1,032 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 0.10 (1032 hom., cov: 32)
• Consequence: LOC107983974 XR_001751681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.937

Genes affected

LOC107983974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1032+5871T>G		intron_variant, non_coding_transcript_variant
LOC107983974	XR_001751679.2	n.6903T>G		non_coding_transcript_exon_variant	5/5
LOC107983974	XR_001751680.2	n.6782T>G		non_coding_transcript_exon_variant	5/5
LOC107983974	XR_007064771.1	n.6337T>G		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000554318.2	n.324+5245T>G		intron_variant, non_coding_transcript_variant		3
	ENST00000653322.2	n.964+5871T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15762 AN: 152042 Hom.: 1024 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0657

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.104 AC: 15804 AN: 152160 Hom.: 1032 Cov.: 32 AF XY: 0.105 AC XY: 7785 AN XY: 74392

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0566

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0880 Hom.: 94

Bravo AF: 0.114

Asia WGS AF: 0.186 AC: 645 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	10
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12437854; hg19: chr15-94141833;