chr8-8726643-A-C

Variant names:

• chr8-8726643-A-C
• rs11780672
• ENST00000522213.5:n.625-2909T>G

Variant summary

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

The ENST00000522213.5(ENSG00000254367):​n.625-2909T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,184 control chromosomes in the GnomAD database, including 1,586 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 (1586 hom., cov: 33)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 9 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.173 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.625-2909T>G		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.456-2909T>G		intron	N/A
	ENSG00000254367	ENST00000765579.1		n.407-1604T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18457 AN: 152066 Hom.: 1586 Cov.: 33

Gnomad AFR AF: 0.0312

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0870

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0501

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.121 AC: 18460 AN: 152184 Hom.: 1586 Cov.: 33 AF XY: 0.122 AC XY: 9080 AN XY: 74406

African (AFR) AF: 0.0311 AC: 1291 AN: 41544

American (AMR) AF: 0.0869 AC: 1328 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3472

East Asian (EAS) AF: 0.0500 AC: 259 AN: 5180

South Asian (SAS) AF: 0.183 AC: 885 AN: 4828

European-Finnish (FIN) AF: 0.170 AC: 1801 AN: 10598

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

European-Non Finnish (NFE) AF: 0.176 AC: 11929 AN: 67960

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.154 Hom.: 8847

Bravo AF: 0.107

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.32
PhyloP100		-1.2

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: rs11780672;

hg19: chr8-8584153;