rs12543698

Positions:

• chr8-108914703-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522244.1(ENSG00000253796):​n.374+3834A>T variant causes a intron, non coding transcript 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: ENST00000522244.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC101927413	XR_928533.3	n.289+1344A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522244.1	n.374+3834A>T		intron_variant, non_coding_transcript_variant		3
	ENST00000524134.1	n.122+1344A>T		intron_variant, non_coding_transcript_variant		5
	ENST00000661381.1	n.123+1344A>T		intron_variant, non_coding_transcript_variant
	ENST00000702172.1	n.289+1344A>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0949

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.193

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12543698; hg19: chr8-109926932;