rs60892987

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-62214946-G-A
• chr11-62214946-G-C
• chr11-62214946-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000254404 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000254404	ENST00000529875.1	n.53-370C>T		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.170

Alfa AF: 0.182 Hom.: 504

Bravo AF: 0.166

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60892987; hg19: chr11-61982418;