4-73778224-T-C

Variant names:

• chr4-73778224-T-C
• rs13109146
• ENST00000779090.1:n.210-494A>G

Variant summary

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

The ENST00000779090.1(ENSG00000301475):​n.210-494A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,026 control chromosomes in the GnomAD database, including 17,840 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 0.44 (17840 hom., cov: 31)
• Consequence: ENSG00000301475 ENST00000779090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394
• Publications: 3 publications found

Genes affected

ENSG00000301475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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
ENSG00000301475	ENST00000779090.1	n.210-494A>G		intron_variant	Intron 2 of 2
ENSG00000301475	ENST00000779091.1	n.116-494A>G		intron_variant	Intron 1 of 1
ENSG00000249051	ENST00000508565.2	n.-164A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67289 AN: 151908 Hom.: 17833 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.443 AC: 67297 AN: 152026 Hom.: 17840 Cov.: 31 AF XY: 0.454 AC XY: 33720 AN XY: 74310

African (AFR) AF: 0.131 AC: 5448 AN: 41490

American (AMR) AF: 0.571 AC: 8723 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2008 AN: 3470

East Asian (EAS) AF: 0.622 AC: 3204 AN: 5152

South Asian (SAS) AF: 0.602 AC: 2896 AN: 4814

European-Finnish (FIN) AF: 0.607 AC: 6406 AN: 10558

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.543 AC: 36930 AN: 67960

Other (OTH) AF: 0.464 AC: 978 AN: 2106

Alfa AF: 0.469 Hom.: 5633

Bravo AF: 0.425

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.0
DANN	Benign	0.76
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs13109146; hg19: chr4-74643941;