ENST00000656144.1:n.3533A>G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254092	ENST00000656144.1	n.3533A>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000254092	ENST00000657283.1	n.2095-11229A>G		intron_variant	Intron 2 of 3
ENSG00000254092	ENST00000657734.1	n.1327-11229A>G		intron_variant	Intron 2 of 4

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

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.842

Alfa AF: 0.829 Hom.: 87210

Bravo AF: 0.853

Asia WGS AF: 0.637 AC: 2218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4961390; hg19: chr8-20928675;