rs12680321

Variant names:

• chr8-76236495-A-C
• rs12680321
• ENST00000668249.2:n.310+69843T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-76236495-A-C
• chr8-76236495-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000668249.2(ENSG00000287352):​n.310+69843T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000287352 ENST00000668249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 1 publications found

Genes affected

ENSG00000287352 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724858	XR_001745961.3	n.286+69843T>G		intron_variant	Intron 2 of 4
LOC102724858	XR_007060967.1	n.298+69843T>G		intron_variant	Intron 2 of 2
LOC102724858	XR_007060968.1	n.281+69843T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287352	ENST00000668249.2	n.310+69843T>G		intron_variant	Intron 2 of 2
ENSG00000287352	ENST00000824976.1	n.251+69843T>G		intron_variant	Intron 2 of 4
ENSG00000287352	ENST00000824977.1	n.259+69843T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 373

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12680321; hg19: chr8-77148730;