3-109679724-G-C

Position:

• chr3-109679724-G-C

Variant summary

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

The ENST00000485384.1(ENSG00000242029):​n.29+31589G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,164 control chromosomes in the GnomAD database, including 52,212 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 0.82 (52212 hom., cov: 32)
• Consequence: ENSG00000242029 ENST00000485384.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78

Genes affected

ENSG00000242029 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906267	XR_007096001.1	n.113-430G>C		intron_variant
LOC124906267	XR_007096002.1	n.113-430G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000242029	ENST00000485384.1	n.29+31589G>C		intron_variant		2
LINC01205	ENST00000658412.1	n.452-430G>C		intron_variant
LINC01205	ENST00000659474.1	n.403-430G>C		intron_variant
LINC01205	ENST00000663929.1	n.489-430G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125262 AN: 152046 Hom.: 52184 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.824 AC: 125340 AN: 152164 Hom.: 52212 Cov.: 32 AF XY: 0.818 AC XY: 60860 AN XY: 74372

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.798

Alfa AF: 0.810 Hom.: 2527

Bravo AF: 0.817

Asia WGS AF: 0.606 AC: 2113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406493; hg19: chr3-109398571;