3-46086150-G-C

Position:

• chr3-46086150-G-C

Variant summary

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

The ENST00000682415.1(ENSG00000288703):​n.76-4288G>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 0.838 in 152,222 control chromosomes in the GnomAD database, including 54,089 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 (54089 hom., cov: 33)
• Consequence: ENST00000682415.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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
	ENST00000682415.1	n.76-4288G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127487 AN: 152104 Hom.: 54025 Cov.: 33

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.989

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.838 AC: 127611 AN: 152222 Hom.: 54089 Cov.: 33 AF XY: 0.842 AC XY: 62678 AN XY: 74406

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.989

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.852

Alfa AF: 0.800 Hom.: 6091

Bravo AF: 0.849

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6767559; hg19: chr3-46127642;