chr21-23857134-A-C

Position:

• chr21-23857134-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661152.1(ENSG00000287612):​n.54A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,230 control chromosomes in the GnomAD database, including 61,702 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 0.90 (61702 hom., cov: 32)
• Consequence: ENSG00000287612 ENST00000661152.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

Genes affected

ENSG00000287612 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372750	XR_937612.2	n.254+1567A>C		intron_variant
LOC105372750	XR_937613.2	n.254+1567A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287612	ENST00000661152.1	n.54A>C		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136846 AN: 152112 Hom.: 61661 Cov.: 32

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.951

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.915

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.900 AC: 136944 AN: 152230 Hom.: 61702 Cov.: 32 AF XY: 0.897 AC XY: 66785 AN XY: 74414

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.862

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.915

Gnomad4 OTH AF: 0.907

Alfa AF: 0.897 Hom.: 2934

Bravo AF: 0.899

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs207553; hg19: chr21-25229450;