8-60049262-G-T

Variant names:

• chr8-60049262-G-T
• rs569688
• ENST00000531077.2:n.131-264G>T

Variant summary

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

The ENST00000531077.2(ENSG00000254775):​n.131-264G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 151,840 control chromosomes in the GnomAD database, including 4,459 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 0.22 (4459 hom., cov: 32)
• Consequence: ENSG00000254775 ENST00000531077.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 13 publications found

Genes affected

ENSG00000254775 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375861	XR_001745714.3	n.131-264G>T		intron_variant	Intron 1 of 4
LOC105375861	XR_001745716.3	n.131-264G>T		intron_variant	Intron 1 of 3
LOC105375861	XR_001745717.3	n.131-264G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254775	ENST00000531077.2	n.131-264G>T		intron_variant	Intron 1 of 5	3
ENSG00000254775	ENST00000655001.1	n.163-264G>T		intron_variant	Intron 1 of 3
ENSG00000254775	ENST00000655977.1	n.137-264G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33589 AN: 151722 Hom.: 4452 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.221 AC: 33617 AN: 151840 Hom.: 4459 Cov.: 32 AF XY: 0.229 AC XY: 16987 AN XY: 74146

African (AFR) AF: 0.121 AC: 5024 AN: 41416

American (AMR) AF: 0.375 AC: 5706 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3472

East Asian (EAS) AF: 0.349 AC: 1795 AN: 5148

South Asian (SAS) AF: 0.172 AC: 827 AN: 4814

European-Finnish (FIN) AF: 0.368 AC: 3866 AN: 10508

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15057 AN: 67938

Other (OTH) AF: 0.205 AC: 433 AN: 2108

Alfa AF: 0.221 Hom.: 16838

Bravo AF: 0.226

Asia WGS AF: 0.275 AC: 956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.65
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs569688; hg19: chr8-60961821;