ENST00000812088.1:n.327+3474C>T

Variant names:

• chr19-48962127-G-A
• rs905238
• ENST00000812088.1:n.327+3474C>T

Variant summary

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

The ENST00000812088.1(ENSG00000305635):​n.327+3474C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,034 control chromosomes in the GnomAD database, including 24,247 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 0.56 (24247 hom., cov: 33)
• Consequence: ENSG00000305635 ENST00000812088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 20 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812088.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305635	ENST00000812088.1		n.327+3474C>T		intron	N/A
	ENSG00000305635	ENST00000812089.1		n.471+3150C>T		intron	N/A
	ENSG00000305635	ENST00000812090.1		n.272+2436C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85503 AN: 151916 Hom.: 24218 Cov.: 33

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.563 AC: 85583 AN: 152034 Hom.: 24247 Cov.: 33 AF XY: 0.570 AC XY: 42350 AN XY: 74316

African (AFR) AF: 0.602 AC: 24947 AN: 41444

American (AMR) AF: 0.542 AC: 8286 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1740 AN: 3472

East Asian (EAS) AF: 0.703 AC: 3636 AN: 5172

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4824

European-Finnish (FIN) AF: 0.635 AC: 6723 AN: 10580

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35277 AN: 67954

Other (OTH) AF: 0.538 AC: 1137 AN: 2112

Alfa AF: 0.530 Hom.: 44756

Bravo AF: 0.556

Asia WGS AF: 0.690 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.73
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs905238; hg19: chr19-49465384;