rs1870301

chr15-95067782-C-T

Variant summary

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

The ENST00000615751.4(ENSG00000293024):n.325-1098C>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 0.113 in 152,272 control chromosomes in the GnomAD database, including 1,247 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 0.11 (1247 hom., cov: 33)
• Consequence: ENST00000615751.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370991	XR_002957693.2	n.378-1098C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000615751.4	n.325-1098C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000616940.1	n.36-1098C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000621842.4	n.328-1098C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17247 AN: 152154 Hom.: 1242 Cov.: 33

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0940

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.113 AC: 17259 AN: 152272 Hom.: 1247 Cov.: 33 AF XY: 0.112 AC XY: 8327 AN XY: 74456

Gnomad4 AFR AF: 0.0303

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0944

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.120

Alfa AF: 0.143 Hom.: 984

Bravo AF: 0.108

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.7
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870301; hg19: chr15-95611011;