rs1457947

Variant names:

• chr6-76766568-A-T
• rs1457947
• ENST00000790727.1:n.279+25637T>A

Variant summary

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

The ENST00000790727.1(ENSG00000302959):​n.279+25637T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,936 control chromosomes in the GnomAD database, including 12,219 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 0.40 (12219 hom., cov: 32)
• Consequence: ENSG00000302959 ENST00000790727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 5 publications found

Genes affected

ENSG00000302959 (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 (SAS) allele frequency at 95% confidence interval = 0.531 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
ENSG00000302959	ENST00000790727.1	n.279+25637T>A		intron_variant	Intron 1 of 2
ENSG00000302959	ENST00000790728.1	n.122+25637T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60552 AN: 151818 Hom.: 12223 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.399 AC: 60585 AN: 151936 Hom.: 12219 Cov.: 32 AF XY: 0.406 AC XY: 30119 AN XY: 74246

African (AFR) AF: 0.363 AC: 15044 AN: 41442

American (AMR) AF: 0.417 AC: 6358 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.532 AC: 2728 AN: 5132

South Asian (SAS) AF: 0.549 AC: 2650 AN: 4828

European-Finnish (FIN) AF: 0.433 AC: 4581 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.394 AC: 26760 AN: 67914

Other (OTH) AF: 0.401 AC: 849 AN: 2116

Alfa AF: 0.410 Hom.: 1641

Bravo AF: 0.393

Asia WGS AF: 0.485 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1457947; hg19: chr6-77476285;