15-46420173-C-T

Variant names:

• chr15-46420173-C-T
• rs11853869
• ENST00000661853.1:n.45+9820C>T

Variant summary

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

The ENST00000661853.1(ENSG00000287704):​n.45+9820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.913 in 152,246 control chromosomes in the GnomAD database, including 64,239 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 0.91 (64239 hom., cov: 33)
• Consequence: ENSG00000287704 ENST00000661853.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 1 publications found

Genes affected

ENSG00000287704 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661853.1. 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
	ENSG00000287704	ENST00000661853.1		n.45+9820C>T		intron	N/A
	ENSG00000287704	ENST00000686120.1		n.56+9820C>T		intron	N/A
	ENSG00000287704	ENST00000736459.1		n.46+9820C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138987 AN: 152128 Hom.: 64208 Cov.: 33

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.913 AC: 139070 AN: 152246 Hom.: 64239 Cov.: 33 AF XY: 0.913 AC XY: 67986 AN XY: 74432

African (AFR) AF: 0.764 AC: 31706 AN: 41490

American (AMR) AF: 0.915 AC: 14001 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.983 AC: 3412 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5164 AN: 5184

South Asian (SAS) AF: 0.958 AC: 4625 AN: 4828

European-Finnish (FIN) AF: 0.964 AC: 10230 AN: 10612

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66784 AN: 68038

Other (OTH) AF: 0.928 AC: 1962 AN: 2114

Alfa AF: 0.966 Hom.: 33950

Bravo AF: 0.902

Asia WGS AF: 0.943 AC: 3278 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.47
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs11853869; hg19: chr15-46712371;