rs1449043

Variant names:

• chr4-58855141-T-C
• rs1449043
• ENST00000510371.5:n.233-3936A>G

Variant summary

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

The ENST00000510371.5(ENSG00000251339):​n.233-3936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,772 control chromosomes in the GnomAD database, including 4,026 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 0.22 (4026 hom., cov: 31)
• Consequence: ENSG00000251339 ENST00000510371.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 1 publications found

Genes affected

ENSG00000251339 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 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
ENSG00000251339	ENST00000510371.5	n.233-3936A>G		intron_variant	Intron 2 of 2	5
ENSG00000251339	ENST00000510941.5	n.306+2484A>G		intron_variant	Intron 3 of 3	3
ENSG00000251339	ENST00000513551.1	n.237-70880A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33679 AN: 151652 Hom.: 4023 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.222 AC: 33684 AN: 151772 Hom.: 4026 Cov.: 31 AF XY: 0.222 AC XY: 16469 AN XY: 74158

African (AFR) AF: 0.146 AC: 6071 AN: 41450

American (AMR) AF: 0.317 AC: 4810 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 497 AN: 3458

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5142

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4808

European-Finnish (FIN) AF: 0.224 AC: 2365 AN: 10560

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16867 AN: 67888

Other (OTH) AF: 0.213 AC: 447 AN: 2096

Alfa AF: 0.238 Hom.: 7591

Bravo AF: 0.228

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.78
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs1449043; hg19: chr4-59721306;