rs2999547

Variant names:

• chr1-152030187-A-C
• rs2999547
• ENST00000432386.1:n.2919+7678A>C

Variant summary

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

The ENST00000432386.1(ENSG00000229021):​n.2919+7678A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 151,918 control chromosomes in the GnomAD database, including 10,832 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 0.34 (10832 hom., cov: 31)
• Consequence: ENSG00000229021 ENST00000432386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

ENSG00000229021 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 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.2919+7678A>C		intron_variant	Intron 12 of 12	2

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52198 AN: 151800 Hom.: 10818 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.0445

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.344 AC: 52259 AN: 151918 Hom.: 10832 Cov.: 31 AF XY: 0.340 AC XY: 25223 AN XY: 74258

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.0446

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.320

Alfa AF: 0.277 Hom.: 6428

Bravo AF: 0.343

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2999547; hg19: chr1-152002663;