10-57215048-C-G

Variant summary

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

The ENST00000690550.1(ENSG00000289158):n.96+7564G>C 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 0.492 in 151,776 control chromosomes in the GnomAD database, including 22,095 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 0.49 (22095 hom., cov: 32)
• Consequence: ENST00000690550.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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
	ENST00000690550.1	n.96+7564G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74604 AN: 151658 Hom.: 22047 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.492 AC: 74715 AN: 151776 Hom.: 22095 Cov.: 32 AF XY: 0.486 AC XY: 36045 AN XY: 74134

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.459

Alfa AF: 0.409 Hom.: 1849

Bravo AF: 0.511

Asia WGS AF: 0.354 AC: 1227 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.23
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11005694; hg19: chr10-58974808;