rs543864

Variant names:

• chr8-37138389-G-A
• rs543864
• ENST00000744926.1:n.222+5446C>T

Variant summary

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

The ENST00000744926.1(ENSG00000297043):​n.222+5446C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,068 control chromosomes in the GnomAD database, including 30,400 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 0.61 (30400 hom., cov: 32)
• Consequence: ENSG00000297043 ENST00000744926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 4 publications found

Genes affected

ENSG00000297043 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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
ENSG00000297043	ENST00000744926.1	n.222+5446C>T		intron_variant	Intron 2 of 4
ENSG00000297043	ENST00000744927.1	n.525-1745C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92327 AN: 151950 Hom.: 30403 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.607 AC: 92367 AN: 152068 Hom.: 30400 Cov.: 32 AF XY: 0.614 AC XY: 45647 AN XY: 74330

African (AFR) AF: 0.339 AC: 14066 AN: 41456

American (AMR) AF: 0.704 AC: 10768 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2373 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2543 AN: 5172

South Asian (SAS) AF: 0.727 AC: 3497 AN: 4810

European-Finnish (FIN) AF: 0.804 AC: 8513 AN: 10586

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48453 AN: 67966

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.654 Hom.: 13436

Bravo AF: 0.588

Asia WGS AF: 0.575 AC: 2002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.015
DANN	Benign	0.39
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs543864; hg19: chr8-36995907;