chr8-8731984-A-G

Variant names:

• chr8-8731984-A-G
• rs11780486
• ENST00000522213.5:n.625-8250T>C

Variant summary

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

The ENST00000522213.5(ENSG00000254367):​n.625-8250T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,166 control chromosomes in the GnomAD database, including 1,584 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 0.12 (1584 hom., cov: 32)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522213.5. 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	ENST00000522213.5	TSL:2	n.625-8250T>C		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.456-8250T>C		intron	N/A
	ENSG00000254367	ENST00000765579.1		n.407-6945T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18772 AN: 152046 Hom.: 1584 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0477

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.123 AC: 18773 AN: 152166 Hom.: 1584 Cov.: 32 AF XY: 0.123 AC XY: 9174 AN XY: 74374

African (AFR) AF: 0.0323 AC: 1342 AN: 41542

American (AMR) AF: 0.0891 AC: 1363 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 581 AN: 3468

East Asian (EAS) AF: 0.0477 AC: 247 AN: 5182

South Asian (SAS) AF: 0.152 AC: 733 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1826 AN: 10568

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12261 AN: 67972

Other (OTH) AF: 0.136 AC: 288 AN: 2110

Alfa AF: 0.144 Hom.: 336

Bravo AF: 0.110

Asia WGS AF: 0.0870 AC: 303 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	2.2
DANN	Benign	0.47
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs11780486; hg19: chr8-8589494;