rs2999547

Positions:

• chr1-152030187-A-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, non coding transcript 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: ENST00000432386.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432386.1	n.2919+7678A>C		intron_variant, non_coding_transcript_variant		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;