3-146914377-T-C

Position:

• chr3-146914377-T-C

Variant summary

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

The ENST00000473299.1(ENSG00000243620):​n.544-4666A>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 0.117 in 152,156 control chromosomes in the GnomAD database, including 1,170 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 0.12 (1170 hom., cov: 32)
• Consequence: ENST00000473299.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000473299.1	n.544-4666A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17814 AN: 152038 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0905

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.0659

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.117 AC: 17840 AN: 152156 Hom.: 1170 Cov.: 32 AF XY: 0.114 AC XY: 8466 AN XY: 74392

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.0905

Gnomad4 EAS AF: 0.0413

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.123

Alfa AF: 0.110 Hom.: 114

Bravo AF: 0.123

Asia WGS AF: 0.0850 AC: 296 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12629805; hg19: chr3-146632164;