chr1-151995200-T-A

Variant names:

• chr1-151995200-T-A
• rs4845720
• ENST00000432386.1:n.76+594T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000432386.1(ENSG00000229021):​n.76+594T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 152,266 control chromosomes in the GnomAD database, including 163 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 0.041 (163 hom., cov: 30)
• Consequence: ENSG00000229021 ENST00000432386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512

Genes affected

ENSG00000229021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0706 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
ENSG00000229021	ENST00000432386.1	n.76+594T>A		intron_variant	Intron 1 of 12	2

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6242 AN: 152148 Hom.: 160 Cov.: 30

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0273

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0411 AC: 6252 AN: 152266 Hom.: 163 Cov.: 30 AF XY: 0.0393 AC XY: 2923 AN XY: 74450

Gnomad4 AFR AF: 0.0728

Gnomad4 AMR AF: 0.0256

Gnomad4 ASJ AF: 0.00606

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.0129

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0329

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0404 Hom.: 13

Bravo AF: 0.0424

Asia WGS AF: 0.0480 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.7
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4845720; hg19: chr1-151967676;