chr21-15440893-T-C

Position:

• chr21-15440893-T-C

Variant summary

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

The ENST00000634644.1(ENSG00000229425):​n.952+26395A>G 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 0.462 in 152,012 control chromosomes in the GnomAD database, including 17,039 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 0.46 (17039 hom., cov: 32)
• Consequence: ENST00000634644.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927745	XR_007067931.1	n.468+3131A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634644.1	n.952+26395A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70165 AN: 151894 Hom.: 17002 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.462 AC: 70258 AN: 152012 Hom.: 17039 Cov.: 32 AF XY: 0.455 AC XY: 33817 AN XY: 74302

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.462

Alfa AF: 0.428 Hom.: 28640

Bravo AF: 0.471

Asia WGS AF: 0.356 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1736148; hg19: chr21-16813212;