chr3-42266417-G-T

Position:

• chr3-42266417-G-T

Variant summary

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

The ENST00000631079.2(ENSG00000281160):​n.1433G>T 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 0.537 in 152,026 control chromosomes in the GnomAD database, including 22,211 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 0.54 (22209 hom., cov: 32)
  • Exomes 𝑓: 0.47 (2 hom.)
• Consequence: ENST00000631079.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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
	ENST00000631079.2	n.1433G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81565 AN: 151886 Hom.: 22192 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.559

GnomAD4 exome AF: 0.467 AC: 14 AN: 30 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.400

GnomAD4 genome AF: 0.537 AC: 81619 AN: 151996 Hom.: 22209 Cov.: 32 AF XY: 0.543 AC XY: 40327 AN XY: 74276

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.560

Alfa AF: 0.531 Hom.: 3226

Bravo AF: 0.536

Asia WGS AF: 0.606 AC: 2094 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13069836; hg19: chr3-42307909;