rs9552241

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000790495.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000277020	ENST00000790495.1		n.925-1181C>G		intron	N/A
	ENSG00000277020	ENST00000790496.1		n.294-1181C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9552241;

hg19: chr13-21127569;

COSMIC: COSV59173085;