8-109008001-T-C

Variant names:

• chr8-109008001-T-C
• rs4735081
• ENST00000522244.1:n.264+35676A>G

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.264+35676A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,046 control chromosomes in the GnomAD database, including 9,311 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 0.34 (9311 hom., cov: 33)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 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.264+35676A>G		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50989 AN: 151932 Hom.: 9302 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.336 AC: 51022 AN: 152046 Hom.: 9311 Cov.: 33 AF XY: 0.333 AC XY: 24754 AN XY: 74348

African (AFR) AF: 0.436 AC: 18078 AN: 41468

American (AMR) AF: 0.231 AC: 3535 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1021 AN: 3470

East Asian (EAS) AF: 0.633 AC: 3272 AN: 5166

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4816

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10564

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19467 AN: 67968

Other (OTH) AF: 0.290 AC: 611 AN: 2110

Alfa AF: 0.292 Hom.: 19275

Bravo AF: 0.340

Asia WGS AF: 0.500 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.64
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs4735081; hg19: chr8-110020230;