3-6093149-T-C

Variant names:

• chr3-6093149-T-C
• rs1504034
• ENST00000425894.2:n.1011-30827T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425894.2(ENSG00000229642):​n.1011-30827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,150 control chromosomes in the GnomAD database, including 53,496 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 (53496 hom., cov: 31)
• Consequence: ENSG00000229642 ENST00000425894.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304
• Publications: 6 publications found

Genes affected

ENSG00000229642 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376942	XR_940578.3	n.582+19804T>C		intron_variant	Intron 2 of 3
LOC105376942	XR_940579.2	n.582+19804T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229642	ENST00000425894.2	n.1011-30827T>C		intron_variant	Intron 6 of 8	3
ENSG00000229642	ENST00000779001.1	n.1158-30827T>C		intron_variant	Intron 6 of 7
ENSG00000229642	ENST00000779002.1	n.870+19804T>C		intron_variant	Intron 6 of 7

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127142 AN: 152032 Hom.: 53434 Cov.: 31

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.836 AC: 127264 AN: 152150 Hom.: 53496 Cov.: 31 AF XY: 0.837 AC XY: 62271 AN XY: 74364

African (AFR) AF: 0.927 AC: 38493 AN: 41526

American (AMR) AF: 0.804 AC: 12279 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2780 AN: 3466

East Asian (EAS) AF: 0.769 AC: 3965 AN: 5156

South Asian (SAS) AF: 0.865 AC: 4175 AN: 4824

European-Finnish (FIN) AF: 0.811 AC: 8587 AN: 10584

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54182 AN: 67998

Other (OTH) AF: 0.843 AC: 1782 AN: 2114

Alfa AF: 0.813 Hom.: 42751

Bravo AF: 0.836

Asia WGS AF: 0.823 AC: 2863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.39
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1504034; hg19: chr3-6134836;