rs10220733

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-84737633-G-A
• chr15-84737633-G-C
• chr15-84737633-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285667 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285667	ENST00000648837.1	n.1630+7575C>T		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.466

Alfa AF: 0.435 Hom.: 14569

Bravo AF: 0.504

Asia WGS AF: 0.654 AC: 2265 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10220733; hg19: chr15-85280864;