8-108928148-C-T

Variant names:

• chr8-108928148-C-T
• rs4336584
• ENST00000522244.1:n.265-9502G>A

Variant summary

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

The ENST00000522244.1(ENSG00000253796):​n.265-9502G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 152,008 control chromosomes in the GnomAD database, including 18,314 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 0.46 (18314 hom., cov: 32)
• Consequence: ENSG00000253796 ENST00000522244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522244.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927413	NR_188033.1		n.135-9502G>A		intron	N/A
	LOC101927413	NR_188034.1		n.135-9502G>A		intron	N/A
	LOC101927413	NR_188035.1		n.135-9502G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253796	ENST00000522244.1	TSL:3	n.265-9502G>A		intron	N/A
	ENSG00000253796	ENST00000656015.4		n.146-9502G>A		intron	N/A
	ENSG00000253796	ENST00000702172.1		n.135-9502G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70404 AN: 151888 Hom.: 18253 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.464 AC: 70536 AN: 152008 Hom.: 18314 Cov.: 32 AF XY: 0.470 AC XY: 34914 AN XY: 74302

African (AFR) AF: 0.697 AC: 28922 AN: 41480

American (AMR) AF: 0.497 AC: 7582 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.296 AC: 1530 AN: 5176

South Asian (SAS) AF: 0.528 AC: 2546 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4387 AN: 10552

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23246 AN: 67942

Other (OTH) AF: 0.425 AC: 897 AN: 2112

Alfa AF: 0.374 Hom.: 19259

Bravo AF: 0.474

Asia WGS AF: 0.410 AC: 1424 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.20
PhyloP100		0.035

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4336584;

hg19: chr8-109940377;