ENST00000820896.1:n.91-6450A>G

Variant names:

• chr19-41648308-T-C
• rs2109075
• ENST00000820896.1:n.91-6450A>G

Variant summary

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

The ENST00000820896.1(ENSG00000306768):​n.91-6450A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 151,866 control chromosomes in the GnomAD database, including 23,153 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 0.55 (23153 hom., cov: 31)
• Consequence: ENSG00000306768 ENST00000820896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 9 publications found

Genes affected

ENSG00000306768 (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 (AMR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372405	XR_935972.1	n.170+3194A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306768	ENST00000820896.1	n.91-6450A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83607 AN: 151748 Hom.: 23136 Cov.: 31

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.583

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

GnomAD4 genome AF: 0.551 AC: 83669 AN: 151866 Hom.: 23153 Cov.: 31 AF XY: 0.552 AC XY: 40958 AN XY: 74204

African (AFR) AF: 0.535 AC: 22148 AN: 41390

American (AMR) AF: 0.591 AC: 9029 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2116 AN: 3466

East Asian (EAS) AF: 0.515 AC: 2662 AN: 5166

South Asian (SAS) AF: 0.520 AC: 2501 AN: 4810

European-Finnish (FIN) AF: 0.512 AC: 5381 AN: 10516

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37760 AN: 67936

Other (OTH) AF: 0.580 AC: 1225 AN: 2112

Alfa AF: 0.556 Hom.: 57610

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2109075; hg19: chr19-42152229;