chr8-22679714-G-A

Variant names:

• chr8-22679714-G-A
• rs17088536
• ENST00000566457.1:n.4296C>T

Variant summary

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

The ENST00000566457.1(ENSG00000261026):​n.4296C>T 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 0.0465 in 152,192 control chromosomes in the GnomAD database, including 207 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 0.047 (207 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: ENSG00000261026 ENST00000566457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.04
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000566457.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261026	ENST00000566457.1	TSL:6	n.4296C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309805	ENST00000844055.1		n.93G>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7061 AN: 152064 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0593

GnomAD4 exome AF: 0.100 AC: 1 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 8

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.0465 AC: 7077 AN: 152182 Hom.: 207 Cov.: 32 AF XY: 0.0486 AC XY: 3617 AN XY: 74406

African (AFR) AF: 0.0294 AC: 1222 AN: 41522

American (AMR) AF: 0.0405 AC: 619 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3468

East Asian (EAS) AF: 0.134 AC: 693 AN: 5172

South Asian (SAS) AF: 0.0983 AC: 472 AN: 4802

European-Finnish (FIN) AF: 0.0607 AC: 644 AN: 10602

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3026 AN: 68002

Other (OTH) AF: 0.0639 AC: 135 AN: 2112

Alfa AF: 0.0447 Hom.: 19

Bravo AF: 0.0433

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.74
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs17088536; hg19: chr8-22537227;