chr8-76233346-G-A

Variant names:

• chr8-76233346-G-A
• rs919577
• ENST00000668249.2:n.311-70332C>T

Variant summary

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

The ENST00000668249.2(ENSG00000287352):​n.311-70332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,796 control chromosomes in the GnomAD database, including 28,363 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 0.61 (28363 hom., cov: 30)
• Consequence: ENSG00000287352 ENST00000668249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 3 publications found

Genes affected

ENSG00000287352 (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 (SAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668249.2. 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
	ENSG00000287352	ENST00000668249.2		n.311-70332C>T		intron	N/A
	ENSG00000287352	ENST00000824976.1		n.252-70332C>T		intron	N/A
	ENSG00000287352	ENST00000824977.1		n.260-70332C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92212 AN: 151678 Hom.: 28356 Cov.: 30

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.608 AC: 92269 AN: 151796 Hom.: 28363 Cov.: 30 AF XY: 0.604 AC XY: 44772 AN XY: 74146

African (AFR) AF: 0.675 AC: 27924 AN: 41392

American (AMR) AF: 0.573 AC: 8745 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2168 AN: 5086

South Asian (SAS) AF: 0.694 AC: 3335 AN: 4804

European-Finnish (FIN) AF: 0.538 AC: 5672 AN: 10548

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40429 AN: 67932

Other (OTH) AF: 0.607 AC: 1280 AN: 2110

Alfa AF: 0.597 Hom.: 86139

Bravo AF: 0.610

Asia WGS AF: 0.567 AC: 1972 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	2.7
DANN	Benign	0.58
PhyloP100		0.28

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: rs919577;

hg19: chr8-77145581;