rs1449043

Positions:

• chr4-58855141-T-C

Variant summary

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

The ENST00000513551.1(ENSG00000251339):​n.237-70880A>G 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 0.222 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: ENST00000513551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000513551.1	n.237-70880A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000510371.5	n.233-3936A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000510941.5	n.306+2484A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.213

Alfa AF: 0.242 Hom.: 5680

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1449043; hg19: chr4-59721306;