8-22680871-T-C

Variant names:

• chr8-22680871-T-C
• rs10104039
• ENST00000566457.1:n.3139A>G

Variant summary

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

The ENST00000844055.1(ENSG00000309805):​n.666T>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 0.589 in 151,788 control chromosomes in the GnomAD database, including 26,635 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 0.59 (26627 hom., cov: 33)
  • Exomes 𝑓: 0.48 (8 hom.)
• Consequence: ENSG00000309805 ENST00000844055.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 15 publications found

Genes affected

ENSG00000261026 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844055.1. 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
	ENSG00000261026	ENST00000566457.1	TSL:6	n.3139A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309805	ENST00000844055.1		n.666T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89308 AN: 151616 Hom.: 26605 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.481 AC: 26 AN: 54 Hom.: 8 Cov.: 0 AF XY: 0.524 AC XY: 22 AN XY: 42

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 4 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.550 AC: 22 AN: 40

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.589 AC: 89363 AN: 151734 Hom.: 26627 Cov.: 33 AF XY: 0.593 AC XY: 44002 AN XY: 74192

African (AFR) AF: 0.506 AC: 20969 AN: 41458

American (AMR) AF: 0.642 AC: 9806 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.655 AC: 3390 AN: 5176

South Asian (SAS) AF: 0.528 AC: 2543 AN: 4816

European-Finnish (FIN) AF: 0.674 AC: 7110 AN: 10546

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41513 AN: 67670

Other (OTH) AF: 0.590 AC: 1248 AN: 2114

Alfa AF: 0.603 Hom.: 51908

Bravo AF: 0.588

Asia WGS AF: 0.544 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.3
DANN	Benign	0.76
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10104039; hg19: chr8-22538384;