11-71389168-A-G

Variant names:

• chr11-71389168-A-G
• rs1790318
• ENST00000460880.1:n.972+166T>C

Variant summary

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

The ENST00000460880.1(ACTE1P):​n.972+166T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,644 control chromosomes in the GnomAD database, including 27,207 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 0.56 (27207 hom., cov: 31)
• Consequence: ACTE1P ENST00000460880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05
• Publications: 6 publications found

Genes affected

ACTE1P (HGNC:51491): (actin epsilon 1, pseudogene)

ACTE1P (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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
ACTE1P	ENST00000460880.1	n.972+166T>C		intron_variant	Intron 7 of 7	6
ACTE1P	ENST00000640065.2	n.1359+166T>C		intron_variant	Intron 10 of 10	5

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85082 AN: 151526 Hom.: 27140 Cov.: 31

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.562 AC: 85220 AN: 151644 Hom.: 27207 Cov.: 31 AF XY: 0.564 AC XY: 41727 AN XY: 74028

African (AFR) AF: 0.852 AC: 35234 AN: 41368

American (AMR) AF: 0.563 AC: 8567 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3466

East Asian (EAS) AF: 0.844 AC: 4337 AN: 5136

South Asian (SAS) AF: 0.637 AC: 3061 AN: 4804

European-Finnish (FIN) AF: 0.371 AC: 3875 AN: 10448

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27050 AN: 67888

Other (OTH) AF: 0.523 AC: 1102 AN: 2108

Alfa AF: 0.498 Hom.: 3608

Bravo AF: 0.589

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.051
DANN	Benign	0.26
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1790318; hg19: chr11-71100214;