rs73013527

Variant names:

• chr11-128627057-C-T
• rs73013527
• ENST00000602773.2:n.208-6283G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647054.1(ENSG00000245008):​n.596-6283G>A variant causes a intron 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: ENSG00000245008 ENST00000647054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 28 publications found

Genes affected

ENSG00000245008 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647054.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000245008	ENST00000602773.2	TSL:6	n.208-6283G>A		intron	N/A
	ENSG00000245008	ENST00000647054.1		n.596-6283G>A		intron	N/A
	ENSG00000245008	ENST00000834815.1		n.227-6283G>A		intron	N/A

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

African (AFR) AF: 0.143 AC: 5939 AN: 41464

American (AMR) AF: 0.411 AC: 6282 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1416 AN: 3464

East Asian (EAS) AF: 0.332 AC: 1713 AN: 5166

South Asian (SAS) AF: 0.359 AC: 1726 AN: 4810

European-Finnish (FIN) AF: 0.574 AC: 6049 AN: 10542

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32568 AN: 67930

Other (OTH) AF: 0.384 AC: 811 AN: 2110

Alfa AF: 0.425 Hom.: 25866

Bravo AF: 0.354

Asia WGS AF: 0.375 AC: 1303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.68
PhyloP100		-0.079

Splicing

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

Other links and lift over

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