ENST00000572256.1:n.421-2828T>C

Variant names:

• chr11-128632601-A-G
• rs4936059
• ENST00000572256.1:n.421-2828T>C

Variant summary

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

The ENST00000572256.1(ENSG00000245008):​n.421-2828T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,120 control chromosomes in the GnomAD database, including 11,547 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 (11547 hom., cov: 33)
• Consequence: ENSG00000245008 ENST00000572256.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 16 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000572256.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000245008	ENST00000572256.1	TSL:4	n.421-2828T>C		intron	N/A
	ENSG00000245008	ENST00000602773.2	TSL:6	n.208-11827T>C		intron	N/A
	ENSG00000245008	ENST00000647054.1		n.596-11827T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58343 AN: 152000 Hom.: 11521 Cov.: 33

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.384 AC: 58408 AN: 152120 Hom.: 11547 Cov.: 33 AF XY: 0.391 AC XY: 29078 AN XY: 74346

African (AFR) AF: 0.384 AC: 15922 AN: 41476

American (AMR) AF: 0.510 AC: 7794 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1196 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2948 AN: 5168

South Asian (SAS) AF: 0.479 AC: 2313 AN: 4824

European-Finnish (FIN) AF: 0.367 AC: 3884 AN: 10588

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23090 AN: 67988

Other (OTH) AF: 0.371 AC: 781 AN: 2106

Alfa AF: 0.355 Hom.: 43268

Bravo AF: 0.393

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4936059; hg19: chr11-128502496;