rs60892987

Positions:

• 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, non coding transcript 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: ENST00000529875.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000529875.1	n.53-370C>T		intron_variant, non_coding_transcript_variant		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;