ENST00000648837.1:n.1630+7575C>T

Variant names:

• chr15-84737633-G-A
• rs10220733
• ENST00000648837.1:n.1630+7575C>T

Variant summary

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

The ENST00000648837.1(ENSG00000285667):​n.1630+7575C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 152,008 control chromosomes in the GnomAD database, including 19,412 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 0.50 (19412 hom., cov: 32)
• Consequence: ENSG00000285667 ENST00000648837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 12 publications found

Genes affected

ENSG00000285667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648837.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285667	ENST00000648837.1		n.1630+7575C>T		intron	N/A
	ENSG00000285667	ENST00000809679.1		n.446+10175C>T		intron	N/A
	ENSG00000285667	ENST00000809680.1		n.441-685C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76003 AN: 151890 Hom.: 19396 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.500 AC: 76060 AN: 152008 Hom.: 19412 Cov.: 32 AF XY: 0.504 AC XY: 37448 AN XY: 74300

African (AFR) AF: 0.568 AC: 23532 AN: 41454

American (AMR) AF: 0.497 AC: 7596 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1476 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4086 AN: 5180

South Asian (SAS) AF: 0.540 AC: 2604 AN: 4826

European-Finnish (FIN) AF: 0.456 AC: 4800 AN: 10536

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30581 AN: 67954

Other (OTH) AF: 0.466 AC: 983 AN: 2110

Alfa AF: 0.445 Hom.: 19827

Bravo AF: 0.504

Asia WGS AF: 0.654 AC: 2265 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.62
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs10220733; hg19: chr15-85280864;