ENST00000455011.3:n.157+21979T>A

Variant names:

• chr6-140876209-A-T
• rs6570426
• ENST00000455011.3:n.157+21979T>A

Variant summary

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

The ENST00000455011.3(ENSG00000234147):​n.157+21979T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,910 control chromosomes in the GnomAD database, including 12,101 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 0.39 (12101 hom., cov: 32)
• Consequence: ENSG00000234147 ENST00000455011.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 4 publications found

Genes affected

ENSG00000234147 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901413	XR_007059792.1	n.322-3348A>T		intron_variant	Intron 2 of 2
LOC102723724	XR_428030.5	n.237+21979T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234147	ENST00000455011.3	n.157+21979T>A		intron_variant	Intron 2 of 3	5
ENSG00000234147	ENST00000650553.2	n.194+21979T>A		intron_variant	Intron 1 of 4
ENSG00000234147	ENST00000682196.2	n.161+21979T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58895 AN: 151790 Hom.: 12075 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.388 AC: 58975 AN: 151910 Hom.: 12101 Cov.: 32 AF XY: 0.384 AC XY: 28526 AN XY: 74234

African (AFR) AF: 0.520 AC: 21551 AN: 41418

American (AMR) AF: 0.313 AC: 4773 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1072 AN: 3460

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5156

South Asian (SAS) AF: 0.314 AC: 1513 AN: 4820

European-Finnish (FIN) AF: 0.361 AC: 3802 AN: 10536

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23405 AN: 67940

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.363 Hom.: 1322

Bravo AF: 0.394

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.1
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6570426; hg19: chr6-141197346;