rs1452093

Positions:

• chr21-27372037-A-G

Variant summary

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

The ENST00000420186.2(ENSG00000231236):​n.332-10881T>C 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 0.464 in 151,940 control chromosomes in the GnomAD database, including 18,368 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 (18368 hom., cov: 32)
• Consequence: ENST00000420186.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000420186.2	n.332-10881T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000447384.1	n.391+9224A>G		intron_variant, non_coding_transcript_variant		1
	ENST00000666822.1	n.399+9224A>G		intron_variant, non_coding_transcript_variant
	ENST00000656258.1	n.434+9224A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70504 AN: 151822 Hom.: 18350 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.464 AC: 70538 AN: 151940 Hom.: 18368 Cov.: 32 AF XY: 0.458 AC XY: 34040 AN XY: 74248

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.469

Alfa AF: 0.575 Hom.: 29812

Bravo AF: 0.443

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.24
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1452093; hg19: chr21-28744356;