11-118703966-C-T

Variant names:

• chr11-118703966-C-T
• rs494459
• ENST00000646572.2:n.230-642C>T

Variant summary

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

The ENST00000646572.2(ENSG00000255422):​n.230-642C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,702 control chromosomes in the GnomAD database, including 12,430 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 0.40 (12430 hom., cov: 30)
• Consequence: ENSG00000255422 ENST00000646572.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 53 publications found

Genes affected

ENSG00000255422 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646572.2. 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
	ENSG00000255422	ENST00000646572.2		n.230-642C>T		intron	N/A
	ENSG00000255422	ENST00000702882.1		n.230-713C>T		intron	N/A
	ENSG00000255422	ENST00000775653.1		n.230+3323C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60464 AN: 151582 Hom.: 12414 Cov.: 30

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.399 AC: 60525 AN: 151702 Hom.: 12430 Cov.: 30 AF XY: 0.396 AC XY: 29386 AN XY: 74114

African (AFR) AF: 0.367 AC: 15170 AN: 41358

American (AMR) AF: 0.519 AC: 7893 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3468

East Asian (EAS) AF: 0.377 AC: 1933 AN: 5132

South Asian (SAS) AF: 0.197 AC: 948 AN: 4812

European-Finnish (FIN) AF: 0.402 AC: 4217 AN: 10490

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27523 AN: 67908

Other (OTH) AF: 0.411 AC: 869 AN: 2112

Alfa AF: 0.406 Hom.: 56032

Bravo AF: 0.414

Asia WGS AF: 0.292 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs494459; hg19: chr11-118574675;