ENST00000741943.1:n.584+17191C>T

Variant names:

• chr16-53396388-C-T
• rs12444248
• ENST00000741943.1:n.584+17191C>T

Variant summary

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

The ENST00000741943.1(ENSG00000261804):​n.584+17191C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,010 control chromosomes in the GnomAD database, including 8,130 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 0.30 (8130 hom., cov: 33)
• Consequence: ENSG00000261804 ENST00000741943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 7 publications found

Genes affected

ENSG00000261804 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 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
ENSG00000261804	ENST00000741943.1	n.584+17191C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45226 AN: 151892 Hom.: 8132 Cov.: 33

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.298 AC: 45227 AN: 152010 Hom.: 8130 Cov.: 33 AF XY: 0.301 AC XY: 22399 AN XY: 74314

African (AFR) AF: 0.105 AC: 4353 AN: 41444

American (AMR) AF: 0.370 AC: 5648 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 941 AN: 3464

East Asian (EAS) AF: 0.643 AC: 3330 AN: 5182

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4818

European-Finnish (FIN) AF: 0.376 AC: 3965 AN: 10532

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24373 AN: 67982

Other (OTH) AF: 0.287 AC: 604 AN: 2108

Alfa AF: 0.336 Hom.: 32836

Bravo AF: 0.294

Asia WGS AF: 0.407 AC: 1411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.30
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs12444248; hg19: chr16-53430300;