ENST00000790495.1:n.925-1181C>G

Variant names:

• chr13-20553430-G-C
• rs9552241
• ENST00000790495.1:n.925-1181C>G

Variant summary

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

The ENST00000790495.1(ENSG00000277020):​n.925-1181C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,224 control chromosomes in the GnomAD database, including 6,092 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 0.25 (6092 hom., cov: 33)
• Consequence: ENSG00000277020 ENST00000790495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116
• Publications: 1 publications found

Genes affected

ENSG00000277020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370103	XR_941721.4	n.1209-1181C>G		intron_variant	Intron 5 of 5
LOC105370103	XR_941722.4	n.1209-1185C>G		intron_variant	Intron 5 of 5
LOC105370103	XR_941723.4	n.1209-426C>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000277020	ENST00000790495.1	n.925-1181C>G		intron_variant	Intron 5 of 5
ENSG00000277020	ENST00000790496.1	n.294-1181C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38525 AN: 152108 Hom.: 6079 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.253 AC: 38551 AN: 152224 Hom.: 6092 Cov.: 33 AF XY: 0.264 AC XY: 19674 AN XY: 74406

African (AFR) AF: 0.193 AC: 8031 AN: 41556

American (AMR) AF: 0.407 AC: 6217 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.698 AC: 3604 AN: 5164

South Asian (SAS) AF: 0.463 AC: 2233 AN: 4824

European-Finnish (FIN) AF: 0.269 AC: 2858 AN: 10608

Middle Eastern (MID) AF: 0.185 AC: 54 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14364 AN: 68010

Other (OTH) AF: 0.226 AC: 476 AN: 2106

Alfa AF: 0.233 Hom.: 586

Bravo AF: 0.261

Asia WGS AF: 0.579 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9552241; hg19: chr13-21127569; COSMIC: COSV59173085;