rs1471233

Variant names:

• chr4-58118142-T-C
• rs1471233
• ENST00000514266.2:n.-72A>G

Variant summary

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

The ENST00000514266.2(ENSG00000249105):​n.-72A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,630 control chromosomes in the GnomAD database, including 22,355 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 0.54 (22280 hom., cov: 32)
  • Exomes 𝑓: 0.47 (75 hom.)
• Consequence: ENSG00000249105 ENST00000514266.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 2 publications found

Genes affected

ENSG00000249105 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.599 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
ENSG00000249105	ENST00000514266.2	n.-72A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81652 AN: 151886 Hom.: 22245 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.538

GnomAD4 exome AF: 0.471 AC: 295 AN: 626 Hom.: 75 AF XY: 0.484 AC XY: 155 AN XY: 320

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.250 AC: 7 AN: 28

European-Finnish (FIN) AF: 0.483 AC: 278 AN: 576

Middle Eastern (MID) AF: 0.125 AC: 1 AN: 8

European-Non Finnish (NFE) AF: 0.667 AC: 8 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.538 AC: 81738 AN: 152004 Hom.: 22280 Cov.: 32 AF XY: 0.538 AC XY: 39935 AN XY: 74280

African (AFR) AF: 0.462 AC: 19170 AN: 41454

American (AMR) AF: 0.609 AC: 9287 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5172

South Asian (SAS) AF: 0.459 AC: 2211 AN: 4822

European-Finnish (FIN) AF: 0.574 AC: 6056 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39173 AN: 67982

Other (OTH) AF: 0.542 AC: 1144 AN: 2110

Alfa AF: 0.564 Hom.: 4158

Bravo AF: 0.541

Asia WGS AF: 0.485 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.069
DANN	Benign	0.61
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1471233; hg19: chr4-58984308;