19-21778502-T-C

Variant names:

• chr19-21778502-T-C
• rs4075276
• ENST00000598561.1:n.116-9375A>G

Variant summary

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

The ENST00000598561.1(ENSG00000268184):​n.116-9375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,084 control chromosomes in the GnomAD database, including 36,780 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 0.69 (36780 hom., cov: 31)
• Consequence: ENSG00000268184 ENST00000598561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206

Genes affected

ENSG00000268184 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.751 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
ENSG00000268184	ENST00000598561.1	n.116-9375A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104925 AN: 151966 Hom.: 36769 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.690 AC: 104954 AN: 152084 Hom.: 36780 Cov.: 31 AF XY: 0.691 AC XY: 51330 AN XY: 74336

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.727

Alfa AF: 0.710 Hom.: 10191

Bravo AF: 0.688

Asia WGS AF: 0.611 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075276; hg19: chr19-21961304;