rs12629805

Variant names:

• chr3-146914377-T-C
• rs12629805
• ENST00000473299.1:n.544-4666A>G

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 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: ENSG00000243620 ENST00000473299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

Genes affected

ENSG00000243620 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243620	ENST00000473299.1	n.544-4666A>G		intron_variant	Intron 5 of 5	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;