8-22696108-T-C

Variant names:

• chr8-22696108-T-C
• rs1008949
• ENST00000685420.3:n.1020T>C

Variant summary

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

The ENST00000685420.3(ENSG00000289521):​n.1020T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 151,960 control chromosomes in the GnomAD database, including 33,969 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 0.66 (33969 hom., cov: 31)
• Consequence: ENSG00000289521 ENST00000685420.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 12 publications found

Genes affected

ENSG00000289521 (HGNC:):

ENSG00000253125 (HGNC:58186):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379321	XR_001745832.2	n.615T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289521	ENST00000685420.3	n.1020T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000289521	ENST00000785393.1	n.425T>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289521	ENST00000785394.1	n.316T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100755 AN: 151842 Hom.: 33909 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.664 AC: 100879 AN: 151960 Hom.: 33969 Cov.: 31 AF XY: 0.662 AC XY: 49138 AN XY: 74264

African (AFR) AF: 0.771 AC: 31959 AN: 41436

American (AMR) AF: 0.737 AC: 11256 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2007 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2604 AN: 5160

South Asian (SAS) AF: 0.576 AC: 2767 AN: 4806

European-Finnish (FIN) AF: 0.601 AC: 6347 AN: 10552

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41723 AN: 67948

Other (OTH) AF: 0.671 AC: 1416 AN: 2110

Alfa AF: 0.631 Hom.: 111269

Bravo AF: 0.681

Asia WGS AF: 0.596 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1008949; hg19: chr8-22553621;