ENST00000759357.1:n.200-31060G>A

Variant names:

• chr6-81477120-C-T
• rs1321761
• ENST00000759357.1:n.200-31060G>A

Variant summary

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

The ENST00000759357.1(ENSG00000298959):​n.200-31060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 150,774 control chromosomes in the GnomAD database, including 19,920 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 0.50 (19920 hom., cov: 30)
• Consequence: ENSG00000298959 ENST00000759357.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.557
• Publications: 1 publications found

Genes affected

ENSG00000298959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377871	XR_007059658.1	n.23233+14371G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298959	ENST00000759357.1	n.200-31060G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76119 AN: 150656 Hom.: 19924 Cov.: 30

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.505 AC: 76125 AN: 150774 Hom.: 19920 Cov.: 30 AF XY: 0.504 AC XY: 37048 AN XY: 73562

African (AFR) AF: 0.363 AC: 14959 AN: 41246

American (AMR) AF: 0.532 AC: 8014 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1835 AN: 3442

East Asian (EAS) AF: 0.448 AC: 2280 AN: 5090

South Asian (SAS) AF: 0.504 AC: 2424 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5328 AN: 10420

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39545 AN: 67402

Other (OTH) AF: 0.496 AC: 1037 AN: 2092

Alfa AF: 0.550 Hom.: 12194

Bravo AF: 0.503

Asia WGS AF: 0.452 AC: 1574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.61
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1321761; hg19: chr6-82186837;