3-21224638-A-T

Position:

• chr3-21224638-A-T

Variant summary

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

The ENST00000634947.1(ENSG00000282987):​n.370+50T>A 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 0.841 in 152,204 control chromosomes in the GnomAD database, including 53,952 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 0.84 (53952 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000634947.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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
	ENST00000634947.1	n.370+50T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127854 AN: 152084 Hom.: 53909 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.841 AC: 127955 AN: 152202 Hom.: 53952 Cov.: 32 AF XY: 0.844 AC XY: 62803 AN XY: 74420

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.830

Alfa AF: 0.825 Hom.: 6064

Bravo AF: 0.846

Asia WGS AF: 0.946 AC: 3288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727611; hg19: chr3-21266130;