rs10517273

chr4-33201720-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653925.1(ENSG00000287968):n.38-960C>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 0.0589 in 152,024 control chromosomes in the GnomAD database, including 587 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 0.059 (587 hom., cov: 32)
• Consequence: ENST00000653925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000653925.1	n.38-960C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0588 AC: 8931 AN: 151908 Hom.: 581 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0164

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0162

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0589 AC: 8959 AN: 152024 Hom.: 587 Cov.: 32 AF XY: 0.0573 AC XY: 4260 AN XY: 74314

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0162

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0309 Hom.: 94

Bravo AF: 0.0641

Asia WGS AF: 0.0330 AC: 114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517273; hg19: chr4-33203342;