chr19-29603679-G-T

Variant names:

• chr19-29603679-G-T
• rs997554
• ENST00000834806.1:n.181-1164C>A

Variant summary

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

The ENST00000834806.1(ENSG00000308527):​n.181-1164C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,166 control chromosomes in the GnomAD database, including 53,037 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 0.83 (53037 hom., cov: 32)
• Consequence: ENSG00000308527 ENST00000834806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 4 publications found

Genes affected

ENSG00000308527 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.836 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
ENSG00000308527	ENST00000834806.1	n.181-1164C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126944 AN: 152048 Hom.: 53000 Cov.: 32

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.851

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.835 AC: 127031 AN: 152166 Hom.: 53037 Cov.: 32 AF XY: 0.837 AC XY: 62237 AN XY: 74388

African (AFR) AF: 0.808 AC: 33522 AN: 41496

American (AMR) AF: 0.847 AC: 12950 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.935 AC: 3248 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4322 AN: 5178

South Asian (SAS) AF: 0.849 AC: 4083 AN: 4812

European-Finnish (FIN) AF: 0.835 AC: 8836 AN: 10582

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57270 AN: 68010

Other (OTH) AF: 0.855 AC: 1809 AN: 2116

Alfa AF: 0.841 Hom.: 41056

Bravo AF: 0.834

Asia WGS AF: 0.863 AC: 3002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs997554; hg19: chr19-30094586;