11-62214946-G-A

Variant names:

• chr11-62214946-G-A
• rs60892987
• ENST00000529875.1:n.53-370C>T

Variant summary

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

The ENST00000529875.1(ENSG00000254404):​n.53-370C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,154 control chromosomes in the GnomAD database, including 2,329 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 0.17 (2329 hom., cov: 32)
• Consequence: ENSG00000254404 ENST00000529875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 3 publications found

Genes affected

ENSG00000254404 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000529875.1. 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
	ENSG00000254404	ENST00000529875.1	TSL:2	n.53-370C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25818 AN: 152036 Hom.: 2328 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.170 AC: 25820 AN: 152154 Hom.: 2329 Cov.: 32 AF XY: 0.166 AC XY: 12339 AN XY: 74366

African (AFR) AF: 0.135 AC: 5619 AN: 41494

American (AMR) AF: 0.140 AC: 2140 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1160 AN: 5186

South Asian (SAS) AF: 0.148 AC: 712 AN: 4816

European-Finnish (FIN) AF: 0.130 AC: 1377 AN: 10580

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13670 AN: 67998

Other (OTH) AF: 0.170 AC: 360 AN: 2116

Alfa AF: 0.189 Hom.: 4614

Bravo AF: 0.166

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs60892987; hg19: chr11-61982418;