chr1-181823356-G-A

Variant names:

• chr1-181823356-G-A
• rs1281194
• ENST00000717053.1:n.432+12136C>T

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.432+12136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,776 control chromosomes in the GnomAD database, including 29,637 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 0.62 (29637 hom., cov: 31)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 4 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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
ENSG00000287452	ENST00000717053.1	n.432+12136C>T		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717054.1	n.437+12136C>T		intron_variant	Intron 2 of 3
ENSG00000287452	ENST00000717055.1	n.225+12136C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93772 AN: 151658 Hom.: 29603 Cov.: 31

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.618 AC: 93858 AN: 151776 Hom.: 29637 Cov.: 31 AF XY: 0.615 AC XY: 45602 AN XY: 74164

African (AFR) AF: 0.483 AC: 19975 AN: 41384

American (AMR) AF: 0.643 AC: 9796 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2371 AN: 3458

East Asian (EAS) AF: 0.475 AC: 2436 AN: 5132

South Asian (SAS) AF: 0.621 AC: 2989 AN: 4810

European-Finnish (FIN) AF: 0.639 AC: 6745 AN: 10562

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

European-Non Finnish (NFE) AF: 0.698 AC: 47388 AN: 67890

Other (OTH) AF: 0.649 AC: 1368 AN: 2108

Alfa AF: 0.673 Hom.: 18395

Bravo AF: 0.611

Asia WGS AF: 0.551 AC: 1913 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.24
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs1281194; hg19: chr1-181792491;