19-50744242-T-C

Variant names:

• chr19-50744242-T-C
• rs6509496
• ENST00000808363.1:n.357-3230A>G

Variant summary

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

The ENST00000808363.1(ENSG00000305066):​n.357-3230A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 148,944 control chromosomes in the GnomAD database, including 56,384 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 0.87 (56384 hom., cov: 22)
• Consequence: ENSG00000305066 ENST00000808363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 7 publications found

Genes affected

ENSG00000305066 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.895 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
ENSG00000305066	ENST00000808363.1	n.357-3230A>G		intron_variant	Intron 2 of 3
ENSG00000305066	ENST00000808364.1	n.362+6218A>G		intron_variant	Intron 2 of 2
ENSG00000305066	ENST00000808365.1	n.206-8479A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 129382 AN: 148838 Hom.: 56333 Cov.: 22

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.869 AC: 129482 AN: 148944 Hom.: 56384 Cov.: 22 AF XY: 0.869 AC XY: 62998 AN XY: 72496

African (AFR) AF: 0.823 AC: 33233 AN: 40372

American (AMR) AF: 0.893 AC: 13238 AN: 14818

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3096 AN: 3464

East Asian (EAS) AF: 0.870 AC: 4375 AN: 5030

South Asian (SAS) AF: 0.918 AC: 4266 AN: 4648

European-Finnish (FIN) AF: 0.872 AC: 8547 AN: 9802

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 59927 AN: 67548

Other (OTH) AF: 0.867 AC: 1789 AN: 2064

Alfa AF: 0.880 Hom.: 181709

Bravo AF: 0.867

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs6509496; hg19: chr19-51247499;