chr8-22680913-C-T

Variant names:

• chr8-22680913-C-T
• rs10095121
• ENST00000566457.1:n.3097G>A

Variant summary

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

The ENST00000844055.1(ENSG00000309805):​n.708C>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 0.695 in 151,978 control chromosomes in the GnomAD database, including 36,928 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 0.70 (36923 hom., cov: 33)
  • Exomes 𝑓: 0.63 (5 hom.)
• Consequence: ENSG00000309805 ENST00000844055.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 12 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 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.3097G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309805	ENST00000844055.1		n.708C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105568 AN: 151828 Hom.: 36881 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.701

GnomAD4 exome AF: 0.625 AC: 20 AN: 32 Hom.: 5 Cov.: 0 AF XY: 0.708 AC XY: 17 AN XY: 24

African (AFR) AF: 1.00 AC: 2 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) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.611 AC: 11 AN: 18

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.695 AC: 105658 AN: 151946 Hom.: 36923 Cov.: 33 AF XY: 0.699 AC XY: 51954 AN XY: 74282

African (AFR) AF: 0.727 AC: 30176 AN: 41490

American (AMR) AF: 0.708 AC: 10807 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3470

East Asian (EAS) AF: 0.797 AC: 4131 AN: 5180

South Asian (SAS) AF: 0.623 AC: 3004 AN: 4824

European-Finnish (FIN) AF: 0.742 AC: 7844 AN: 10572

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45125 AN: 67824

Other (OTH) AF: 0.700 AC: 1478 AN: 2112

Alfa AF: 0.681 Hom.: 24565

Bravo AF: 0.698

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	13
DANN	Benign	0.72
PhyloP100		0.66

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: rs10095121;

hg19: chr8-22538426;