rs10220733

Positions:

• 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, non coding transcript 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: ENST00000648837.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648837.1	n.1630+7575C>T		intron_variant, non_coding_transcript_variant

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;