21-15440233-C-A

Position:

• chr21-15440233-C-A

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.952+27055G>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 0.328 in 151,878 control chromosomes in the GnomAD database, including 9,537 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 0.33 (9537 hom., cov: 31)
• Consequence: ENST00000634644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927745	XR_007067931.1	n.468+3791G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634644.1	n.952+27055G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49814 AN: 151760 Hom.: 9532 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.328 AC: 49828 AN: 151878 Hom.: 9537 Cov.: 31 AF XY: 0.324 AC XY: 24083 AN XY: 74228

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.361

Alfa AF: 0.401 Hom.: 15026

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.7
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736020; hg19: chr21-16812552;