chr19-33240645-G-A

Variant names:

• chr19-33240645-G-A
• rs17694108
• ENST00000762495.1:n.165-800C>T

Variant summary

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

The ENST00000762495.1(ENSG00000299313):​n.165-800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,248 control chromosomes in the GnomAD database, including 4,767 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 0.23 (4767 hom., cov: 34)
• Consequence: ENSG00000299313 ENST00000762495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 48 publications found

Genes affected

ENSG00000299313 (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 (SAS) allele frequency at 95% confidence interval = 0.361 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
ENSG00000299313	ENST00000762495.1	n.165-800C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34531 AN: 152130 Hom.: 4762 Cov.: 34

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.227 AC: 34541 AN: 152248 Hom.: 4767 Cov.: 34 AF XY: 0.232 AC XY: 17264 AN XY: 74440

African (AFR) AF: 0.0625 AC: 2597 AN: 41566

American (AMR) AF: 0.235 AC: 3601 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5166

South Asian (SAS) AF: 0.376 AC: 1816 AN: 4832

European-Finnish (FIN) AF: 0.355 AC: 3762 AN: 10604

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19326 AN: 67992

Other (OTH) AF: 0.253 AC: 534 AN: 2114

Alfa AF: 0.268 Hom.: 9462

Bravo AF: 0.207

Asia WGS AF: 0.316 AC: 1098 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	5.3
DANN	Benign	0.52
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs17694108; hg19: chr19-33731551;