rs2999547

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000229021 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000432386.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000229021	ENST00000432386.1	TSL:2	n.2919+7678A>C		intron	N/A
	ENSG00000229021	ENST00000759538.1		n.753+7678A>C		intron	N/A

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

African (AFR) AF: 0.575 AC: 23793 AN: 41352

American (AMR) AF: 0.243 AC: 3713 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3470

East Asian (EAS) AF: 0.0446 AC: 231 AN: 5182

South Asian (SAS) AF: 0.199 AC: 955 AN: 4808

European-Finnish (FIN) AF: 0.329 AC: 3472 AN: 10550

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.273 AC: 18539 AN: 67972

Other (OTH) AF: 0.320 AC: 675 AN: 2108

Alfa AF: 0.282 Hom.: 8068

Bravo AF: 0.343

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.51
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2999547; hg19: chr1-152002663;