8-21071164-T-C

Variant names:

• chr8-21071164-T-C
• rs4961390
• ENST00000656144.1:n.3533A>G

Variant summary

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

The ENST00000656144.1(ENSG00000254092):​n.3533A>G 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 0.847 in 152,228 control chromosomes in the GnomAD database, including 55,377 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 0.85 (55377 hom., cov: 32)
• Consequence: ENSG00000254092 ENST00000656144.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 0 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656144.1. 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
	ENSG00000254092	ENST00000656144.1		n.3533A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000254092	ENST00000518967.2	TSL:2	n.246-11229A>G		intron	N/A
	ENSG00000254092	ENST00000657283.1		n.2095-11229A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128759 AN: 152110 Hom.: 55330 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.847 AC: 128866 AN: 152228 Hom.: 55377 Cov.: 32 AF XY: 0.840 AC XY: 62521 AN XY: 74420

African (AFR) AF: 0.960 AC: 39899 AN: 41556

American (AMR) AF: 0.789 AC: 12071 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2905 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2566 AN: 5158

South Asian (SAS) AF: 0.765 AC: 3689 AN: 4824

European-Finnish (FIN) AF: 0.783 AC: 8299 AN: 10594

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56641 AN: 68010

Other (OTH) AF: 0.842 AC: 1779 AN: 2114

Alfa AF: 0.838 Hom.: 144794

Bravo AF: 0.853

Asia WGS AF: 0.637 AC: 2218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.54
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4961390; hg19: chr8-20928675;