rs6481257

chr10-57178792-C-A

Variant summary

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

The ENST00000690550.1(ENSG00000289158):n.96+43820G>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 0.45 in 151,704 control chromosomes in the GnomAD database, including 19,608 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 0.45 (19608 hom., cov: 31)
• Consequence: ENST00000690550.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 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+43820G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68181 AN: 151586 Hom.: 19559 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.450 AC: 68286 AN: 151704 Hom.: 19608 Cov.: 31 AF XY: 0.447 AC XY: 33123 AN XY: 74084

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.424

Alfa AF: 0.322 Hom.: 14784

Bravo AF: 0.468

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.71
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6481257; hg19: chr10-58938552;