rs1870301

Variant names:

• chr15-95067782-C-T
• rs1870301
• ENST00000615751.5:n.381-1098C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000831759.1(ENSG00000293024):​n.361-1098C>T variant causes a intron 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: ENSG00000293024 ENST00000831759.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 4 publications found

Genes affected

ENSG00000293024 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831759.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293024	ENST00000615751.5	TSL:5	n.381-1098C>T		intron	N/A
	ENSG00000293024	ENST00000616940.1	TSL:5	n.36-1098C>T		intron	N/A
	ENSG00000293024	ENST00000621842.4	TSL:5	n.328-1098C>T		intron	N/A

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

African (AFR) AF: 0.0303 AC: 1261 AN: 41554

American (AMR) AF: 0.127 AC: 1949 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3470

East Asian (EAS) AF: 0.103 AC: 536 AN: 5188

South Asian (SAS) AF: 0.0944 AC: 456 AN: 4828

European-Finnish (FIN) AF: 0.155 AC: 1647 AN: 10592

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10799 AN: 68018

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.141 Hom.: 1269

Bravo AF: 0.108

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		-0.28

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1870301;

hg19: chr15-95611011;