19-48952897-G-T

Variant names:

• chr19-48952897-G-T
• rs11667351
• ENST00000812088.1:n.328-2572C>A

Variant summary

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

The ENST00000812088.1(ENSG00000305635):​n.328-2572C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.858 in 150,944 control chromosomes in the GnomAD database, including 55,608 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 0.86 (55608 hom., cov: 27)
• Consequence: ENSG00000305635 ENST00000812088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 14 publications found

Genes affected

ENSG00000305635 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 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
ENSG00000305635	ENST00000812088.1	n.328-2572C>A		intron_variant	Intron 1 of 1
ENSG00000305635	ENST00000812089.1	n.472-2572C>A		intron_variant	Intron 2 of 2
ENSG00000305635	ENST00000812090.1	n.273-2572C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.858 AC: 129340 AN: 150826 Hom.: 55554 Cov.: 27

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.858 AC: 129450 AN: 150944 Hom.: 55608 Cov.: 27 AF XY: 0.861 AC XY: 63392 AN XY: 73630

African (AFR) AF: 0.813 AC: 33326 AN: 40976

American (AMR) AF: 0.825 AC: 12420 AN: 15048

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3093 AN: 3466

East Asian (EAS) AF: 0.950 AC: 4883 AN: 5142

South Asian (SAS) AF: 0.910 AC: 4367 AN: 4800

European-Finnish (FIN) AF: 0.920 AC: 9447 AN: 10272

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.871 AC: 59172 AN: 67928

Other (OTH) AF: 0.846 AC: 1783 AN: 2108

Alfa AF: 0.868 Hom.: 54020

Bravo AF: 0.846

Asia WGS AF: 0.880 AC: 3061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.79
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11667351; hg19: chr19-49456154;