ENST00000412563.1:n.357-3605C>T

Variant names:

• chr7-19572682-C-T
• rs2192476
• ENST00000412563.1:n.357-3605C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000412563.1(ENSG00000223838):​n.357-3605C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 151,888 control chromosomes in the GnomAD database, including 20,359 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 0.47 (20359 hom., cov: 32)
• Consequence: ENSG00000223838 ENST00000412563.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110
• Publications: 6 publications found

Genes affected

ENSG00000223838 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412563.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000223838	ENST00000412563.1	TSL:5	n.357-3605C>T		intron	N/A
	ENSG00000223838	ENST00000779060.1		n.83-5847C>T		intron	N/A
	ENSG00000223838	ENST00000779061.1		n.237-5847C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71802 AN: 151770 Hom.: 20352 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.473 AC: 71819 AN: 151888 Hom.: 20359 Cov.: 32 AF XY: 0.470 AC XY: 34860 AN XY: 74226

African (AFR) AF: 0.186 AC: 7708 AN: 41440

American (AMR) AF: 0.455 AC: 6931 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2100 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5152

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4812

European-Finnish (FIN) AF: 0.713 AC: 7546 AN: 10578

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.635 AC: 43135 AN: 67914

Other (OTH) AF: 0.490 AC: 1031 AN: 2106

Alfa AF: 0.440 Hom.: 1540

Bravo AF: 0.444

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.56
PhyloP100		-0.011

Splicing

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

Other links and lift over

dbSNP: rs2192476; hg19: chr7-19612305;