ENST00000522244.1:n.130-7804C>A

Variant names:

• chr8-109051931-G-T
• rs4276659
• ENST00000522244.1:n.130-7804C>A

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.130-7804C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 152,080 control chromosomes in the GnomAD database, including 31,744 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 0.64 (31744 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.329

Genes affected

ENSG00000253796 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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
ENSG00000253796	ENST00000522244.1	n.130-7804C>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96858 AN: 151962 Hom.: 31708 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.637 AC: 96949 AN: 152080 Hom.: 31744 Cov.: 32 AF XY: 0.639 AC XY: 47473 AN XY: 74326

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.618

Alfa AF: 0.550 Hom.: 3228

Bravo AF: 0.660

Asia WGS AF: 0.675 AC: 2346 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	1.3
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4276659; hg19: chr8-110064160;