rs73013527

chr11-128627057-C-T

Variant summary

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

The ENST00000647054.1(ENSG00000245008):n.596-6283G>A 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 0.376 in 151,980 control chromosomes in the GnomAD database, including 12,484 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 0.38 (12484 hom., cov: 31)
• Consequence: ENST00000647054.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
	ENST00000647054.1	n.596-6283G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57179 AN: 151862 Hom.: 12492 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.376 AC: 57191 AN: 151980 Hom.: 12484 Cov.: 31 AF XY: 0.382 AC XY: 28344 AN XY: 74276

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.384

Alfa AF: 0.419 Hom.: 1840

Bravo AF: 0.354

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73013527; hg19: chr11-128496952; COSMIC: COSV73923906;