chr8-29296260-C-T

Variant names:

• chr8-29296260-C-T
• rs643472
• ENST00000686912.2:n.82-3576G>A

Variant summary

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

The ENST00000686912.2(ENSG00000288735):​n.82-3576G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,046 control chromosomes in the GnomAD database, including 40,954 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 0.73 (40954 hom., cov: 32)
• Consequence: ENSG00000288735 ENST00000686912.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.242
• Publications: 11 publications found

Genes affected

ENSG00000288735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901922	XR_007060873.1	n.87-3553G>A		intron_variant	Intron 1 of 2
LOC124901922	XR_007060874.1	n.87-3576G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288735	ENST00000686912.2	n.82-3576G>A		intron_variant	Intron 1 of 2
ENSG00000288735	ENST00000701393.2	n.232-3576G>A		intron_variant	Intron 1 of 2
ENSG00000288735	ENST00000701969.2	n.95-3553G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111227 AN: 151928 Hom.: 40937 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.732 AC: 111293 AN: 152046 Hom.: 40954 Cov.: 32 AF XY: 0.728 AC XY: 54085 AN XY: 74306

African (AFR) AF: 0.703 AC: 29167 AN: 41468

American (AMR) AF: 0.631 AC: 9642 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2278 AN: 3468

East Asian (EAS) AF: 0.882 AC: 4551 AN: 5160

South Asian (SAS) AF: 0.787 AC: 3795 AN: 4822

European-Finnish (FIN) AF: 0.686 AC: 7234 AN: 10544

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52184 AN: 67998

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.751 Hom.: 125158

Bravo AF: 0.724

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.40
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs643472; hg19: chr8-29153777;