rs12543698

Variant names:

• chr8-108914703-T-A
• rs12543698
• ENST00000522244.1:n.374+3834A>T

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.374+3834A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,054 control chromosomes in the GnomAD database, including 3,288 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 0.19 (3288 hom., cov: 31)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 1 publications found

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927413	NR_188034.1	n.289+1344A>T		intron_variant	Intron 3 of 3
LOC101927413	NR_188035.1	n.289+1344A>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253796	ENST00000522244.1	n.374+3834A>T		intron_variant	Intron 4 of 4	3
ENSG00000253796	ENST00000524134.1	n.122+1344A>T		intron_variant	Intron 2 of 4	5
ENSG00000253796	ENST00000661381.1	n.123+1344A>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29489 AN: 151940 Hom.: 3280 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.194 AC: 29507 AN: 152054 Hom.: 3288 Cov.: 31 AF XY: 0.199 AC XY: 14781 AN XY: 74294

African (AFR) AF: 0.131 AC: 5446 AN: 41500

American (AMR) AF: 0.345 AC: 5269 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 639 AN: 3462

East Asian (EAS) AF: 0.0949 AC: 492 AN: 5186

South Asian (SAS) AF: 0.185 AC: 890 AN: 4816

European-Finnish (FIN) AF: 0.242 AC: 2559 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13653 AN: 67960

Other (OTH) AF: 0.193 AC: 408 AN: 2110

Alfa AF: 0.200 Hom.: 416

Bravo AF: 0.198

Asia WGS AF: 0.107 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs12543698; hg19: chr8-109926932;