rs4936059

Positions:

• 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 ENST00000647054.1(ENSG00000245008):​n.596-11827T>C 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 0.384 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: ENST00000647054.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000647054.1	n.596-11827T>C		intron_variant, non_coding_transcript_variant
	ENST00000572256.1	n.421-2828T>C		intron_variant, non_coding_transcript_variant		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;