rs1355459

Variant names:

• chr6-23871472-G-A
• rs1355459
• ENST00000790555.1:n.464-3224G>A

Variant summary

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

The ENST00000790555.1(ENSG00000290589):​n.464-3224G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,784 control chromosomes in the GnomAD database, including 7,816 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 0.31 (7816 hom., cov: 32)
• Consequence: ENSG00000290589 ENST00000790555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 4 publications found

Genes affected

ENSG00000290589 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.362 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
ENSG00000290589	ENST00000790555.1	n.464-3224G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47688 AN: 151668 Hom.: 7807 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.314 AC: 47731 AN: 151784 Hom.: 7816 Cov.: 32 AF XY: 0.314 AC XY: 23255 AN XY: 74154

African (AFR) AF: 0.361 AC: 14920 AN: 41370

American (AMR) AF: 0.233 AC: 3551 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.0789 AC: 407 AN: 5156

South Asian (SAS) AF: 0.376 AC: 1810 AN: 4810

European-Finnish (FIN) AF: 0.324 AC: 3399 AN: 10488

Middle Eastern (MID) AF: 0.297 AC: 86 AN: 290

European-Non Finnish (NFE) AF: 0.318 AC: 21587 AN: 67908

Other (OTH) AF: 0.323 AC: 682 AN: 2112

Alfa AF: 0.320 Hom.: 1034

Bravo AF: 0.305

Asia WGS AF: 0.240 AC: 827 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.21
DANN	Benign	0.20
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1355459; hg19: chr6-23871700; COSMIC: COSV69193792;