rs13256369

Variant names:

• chr8-8719869-T-C
• rs13256369
• ENST00000765578.1:n.660+3661A>G

Variant summary

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

The ENST00000765578.1(ENSG00000254367):​n.660+3661A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,152 control chromosomes in the GnomAD database, including 5,735 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 0.27 (5735 hom., cov: 33)
• Consequence: ENSG00000254367 ENST00000765578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 11 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765578.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254367	ENST00000765578.1		n.660+3661A>G		intron	N/A
	ENSG00000254367	ENST00000765579.1		n.741-339A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40433 AN: 152034 Hom.: 5718 Cov.: 33

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.266 AC: 40484 AN: 152152 Hom.: 5735 Cov.: 33 AF XY: 0.274 AC XY: 20358 AN XY: 74360

African (AFR) AF: 0.218 AC: 9072 AN: 41532

American (AMR) AF: 0.308 AC: 4712 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3468

East Asian (EAS) AF: 0.444 AC: 2300 AN: 5180

South Asian (SAS) AF: 0.398 AC: 1920 AN: 4824

European-Finnish (FIN) AF: 0.347 AC: 3664 AN: 10554

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17148 AN: 67988

Other (OTH) AF: 0.258 AC: 544 AN: 2110

Alfa AF: 0.262 Hom.: 4668

Bravo AF: 0.261

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13256369; hg19: chr8-8577379;