chr8-34269430-C-T

Variant names:

• chr8-34269430-C-T
• rs6990255
• ENST00000522460.1:n.203-27829C>T

Variant summary

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

The ENST00000522460.1(ENSG00000253108):​n.203-27829C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0982 in 152,114 control chromosomes in the GnomAD database, including 1,175 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 0.098 (1175 hom., cov: 32)
• Consequence: ENSG00000253108 ENST00000522460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 18 publications found

Genes affected

ENSG00000253108 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.219 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
ENSG00000253108	ENST00000522460.1	n.203-27829C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0982 AC: 14920 AN: 151994 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.0441

Gnomad SAS AF: 0.0337

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.0814

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

GnomAD4 genome AF: 0.0982 AC: 14933 AN: 152114 Hom.: 1175 Cov.: 32 AF XY: 0.0990 AC XY: 7362 AN XY: 74364

African (AFR) AF: 0.222 AC: 9221 AN: 41472

American (AMR) AF: 0.0757 AC: 1157 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00807 AC: 28 AN: 3468

East Asian (EAS) AF: 0.0444 AC: 230 AN: 5178

South Asian (SAS) AF: 0.0337 AC: 163 AN: 4830

European-Finnish (FIN) AF: 0.0851 AC: 900 AN: 10580

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0449 AC: 3051 AN: 67986

Other (OTH) AF: 0.0820 AC: 173 AN: 2110

Alfa AF: 0.0573 Hom.: 1741

Bravo AF: 0.101

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.8
DANN	Benign	0.39
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs6990255; hg19: chr8-34126948;