chr3-133731527-T-G

Position:

• chr3-133731527-T-G

Variant summary

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

The ENST00000460564.5(ENSG00000291042):​n.382-22068T>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 0.587 in 151,980 control chromosomes in the GnomAD database, including 26,700 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 0.59 (26700 hom., cov: 31)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TF	NM_001354703.2	c.-89-16885T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000460564.5	n.382-22068T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89094 AN: 151862 Hom.: 26661 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.587 AC: 89188 AN: 151980 Hom.: 26700 Cov.: 31 AF XY: 0.588 AC XY: 43700 AN XY: 74260

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.557

Alfa AF: 0.536 Hom.: 42527

Bravo AF: 0.599

Asia WGS AF: 0.760 AC: 2643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6439434; hg19: chr3-133450371;