rs4936059

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-128632601-A-G
• chr11-128632601-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000245008 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000245008	ENST00000572256.1	n.421-2828T>C		intron_variant	Intron 3 of 3	4
ENSG00000245008	ENST00000647054.1	n.596-11827T>C		intron_variant	Intron 3 of 4

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

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.479

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.371

Alfa AF: 0.353 Hom.: 19906

Bravo AF: 0.393

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4936059; hg19: chr11-128502496;