ENST00000783209.1:n.163-1111T>G

Variant names:

• chr19-51464613-A-C
• rs11672925
• ENST00000783209.1:n.163-1111T>G

Variant summary

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

The ENST00000783209.1(ENSG00000301984):​n.163-1111T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,014 control chromosomes in the GnomAD database, including 13,362 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 0.40 (13362 hom., cov: 30)
• Consequence: ENSG00000301984 ENST00000783209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

Genes affected

ENSG00000301984 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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
ENSG00000301984	ENST00000783209.1	n.163-1111T>G		intron_variant	Intron 1 of 1
ENSG00000301984	ENST00000783210.1	n.123-1107T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60377 AN: 151896 Hom.: 13355 Cov.: 30

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.397 AC: 60412 AN: 152014 Hom.: 13362 Cov.: 30 AF XY: 0.398 AC XY: 29562 AN XY: 74304

African (AFR) AF: 0.209 AC: 8661 AN: 41468

American (AMR) AF: 0.381 AC: 5822 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1812 AN: 3470

East Asian (EAS) AF: 0.353 AC: 1821 AN: 5164

South Asian (SAS) AF: 0.454 AC: 2184 AN: 4814

European-Finnish (FIN) AF: 0.513 AC: 5410 AN: 10536

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33216 AN: 67972

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.461 Hom.: 30960

Bravo AF: 0.378

Asia WGS AF: 0.402 AC: 1398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.075
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs11672925; hg19: chr19-51967867;