ENST00000431862.1:n.227+18325C>T

Variant names:

• chr1-159450517-G-A
• rs11265198
• ENST00000431862.1:n.227+18325C>T

Variant summary

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

The ENST00000431862.1(ENSG00000228560):​n.227+18325C>T variant causes a intron change. The variant allele was found at a frequency of 0.803 in 151,410 control chromosomes in the GnomAD database, including 54,353 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 0.80 (54353 hom., cov: 29)
• Consequence: ENSG00000228560 ENST00000431862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 7 publications found

Genes affected

ENSG00000228560 (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 (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000228560	ENST00000431862.1	n.227+18325C>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 121620 AN: 151318 Hom.: 54351 Cov.: 29

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.803 AC: 121647 AN: 151410 Hom.: 54353 Cov.: 29 AF XY: 0.809 AC XY: 59873 AN XY: 73986

African (AFR) AF: 0.367 AC: 15075 AN: 41036

American (AMR) AF: 0.915 AC: 13979 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3299 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5160 AN: 5160

South Asian (SAS) AF: 0.973 AC: 4679 AN: 4810

European-Finnish (FIN) AF: 0.989 AC: 10292 AN: 10408

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.974 AC: 66212 AN: 67946

Other (OTH) AF: 0.849 AC: 1787 AN: 2104

Alfa AF: 0.793 Hom.: 10111

Bravo AF: 0.778

Asia WGS AF: 0.951 AC: 3307 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	0.63
DANN	Benign	0.34

Splicing

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

Other links and lift over

dbSNP: rs11265198; hg19: chr1-159420307;