rs496547

Variant names:

• chr11-118705754-A-T
• rs496547
• ENST00000526274.2:n.231+916A>T

Variant summary

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

The ENST00000526274.2(ENSG00000255422):​n.231+916A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.639 in 151,632 control chromosomes in the GnomAD database, including 31,168 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 0.64 (31168 hom., cov: 29)
• Consequence: ENSG00000255422 ENST00000526274.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 17 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526274.2. 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	ENST00000526274.2	TSL:3	n.231+916A>T		intron	N/A
	ENSG00000255422	ENST00000646572.2		n.460+916A>T		intron	N/A
	ENSG00000255422	ENST00000702882.1		n.389+916A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96795 AN: 151518 Hom.: 31132 Cov.: 29

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.639 AC: 96882 AN: 151632 Hom.: 31168 Cov.: 29 AF XY: 0.637 AC XY: 47204 AN XY: 74052

African (AFR) AF: 0.588 AC: 24288 AN: 41274

American (AMR) AF: 0.697 AC: 10601 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2274 AN: 3470

East Asian (EAS) AF: 0.766 AC: 3948 AN: 5152

South Asian (SAS) AF: 0.579 AC: 2778 AN: 4800

European-Finnish (FIN) AF: 0.660 AC: 6910 AN: 10474

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43851 AN: 67936

Other (OTH) AF: 0.659 AC: 1392 AN: 2112

Alfa AF: 0.639 Hom.: 3896

Bravo AF: 0.643

Asia WGS AF: 0.675 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.7
DANN	Benign	0.63
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs496547; hg19: chr11-118576463; COSMIC: COSV65996544;