rs8177185

chr3-133745774-G-A

Variant summary

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

The ENST00000460564.5(ENSG00000291042):n.382-7821G>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 0.0824 in 152,220 control chromosomes in the GnomAD database, including 696 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 0.082 (696 hom., cov: 33)
• Consequence: ENST00000460564.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TF	NM_001354703.2	c.-89-2638G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000460564.5	n.382-7821G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0823 AC: 12521 AN: 152100 Hom.: 691 Cov.: 33

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0515

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.0824 AC: 12540 AN: 152220 Hom.: 696 Cov.: 33 AF XY: 0.0829 AC XY: 6172 AN XY: 74424

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0515

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0610 Hom.: 320

Bravo AF: 0.0910

Asia WGS AF: 0.186 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	11
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8177185; hg19: chr3-133464618;