19-35318897-A-G

Variant names:

• chr19-35318897-A-G
• rs756796
• ENST00000700969.2:n.250+8T>C

Variant summary

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

The ENST00000700969.2(ENSG00000289845):​n.250+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 151,986 control chromosomes in the GnomAD database, including 51,230 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 0.82 (51230 hom., cov: 29)
• Consequence: ENSG00000289845 ENST00000700969.2 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 10 publications found

Genes affected

ENSG00000289845 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 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
ENSG00000289845	ENST00000700969.2	n.250+8T>C		splice_region_variant, intron_variant	Intron 1 of 1
ENSG00000289845	ENST00000827650.1	n.186+8T>C		splice_region_variant, intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.816 AC: 123922 AN: 151868 Hom.: 51165 Cov.: 29

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.816 AC: 124050 AN: 151986 Hom.: 51230 Cov.: 29 AF XY: 0.816 AC XY: 60594 AN XY: 74242

African (AFR) AF: 0.950 AC: 39394 AN: 41484

American (AMR) AF: 0.799 AC: 12200 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2741 AN: 3470

East Asian (EAS) AF: 0.815 AC: 4187 AN: 5138

South Asian (SAS) AF: 0.845 AC: 4067 AN: 4814

European-Finnish (FIN) AF: 0.726 AC: 7650 AN: 10540

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51029 AN: 67958

Other (OTH) AF: 0.838 AC: 1770 AN: 2112

Alfa AF: 0.780 Hom.: 72564

Bravo AF: 0.824

Asia WGS AF: 0.863 AC: 3003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.051
PromoterAI		-0.085	Neutral

Splicing

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

Other links and lift over

dbSNP: rs756796; hg19: chr19-35809800;