ENST00000820896.1:n.91-7228G>A

Variant names:

• chr19-41649086-C-T
• rs2016070
• ENST00000820896.1:n.91-7228G>A

Variant summary

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

The ENST00000820896.1(ENSG00000306768):​n.91-7228G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,014 control chromosomes in the GnomAD database, including 4,483 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 0.24 (4483 hom., cov: 31)
• Consequence: ENSG00000306768 ENST00000820896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372405	XR_935972.1	n.170+2416G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306768	ENST00000820896.1	n.91-7228G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36235 AN: 151896 Hom.: 4479 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.238 AC: 36248 AN: 152014 Hom.: 4483 Cov.: 31 AF XY: 0.234 AC XY: 17386 AN XY: 74306

African (AFR) AF: 0.229 AC: 9494 AN: 41450

American (AMR) AF: 0.215 AC: 3291 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1038 AN: 3464

East Asian (EAS) AF: 0.185 AC: 958 AN: 5174

South Asian (SAS) AF: 0.108 AC: 520 AN: 4820

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10566

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17641 AN: 67952

Other (OTH) AF: 0.255 AC: 538 AN: 2112

Alfa AF: 0.251 Hom.: 1814

Bravo AF: 0.243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2016070; hg19: chr19-42153007;