rs9550855

Variant names:

• chr13-22662653-G-A
• rs9550855
• ENST00000815335.1:n.634C>T

Variant summary

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

The ENST00000815335.1(ENSG00000306102):​n.634C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,992 control chromosomes in the GnomAD database, including 5,357 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 0.26 (5357 hom., cov: 32)
• Consequence: ENSG00000306102 ENST00000815335.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 4 publications found

Genes affected

ENSG00000306102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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
ENSG00000306102	ENST00000815335.1	n.634C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000306102	ENST00000815334.1	n.376+233C>T		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39195 AN: 151876 Hom.: 5357 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.258 AC: 39194 AN: 151992 Hom.: 5357 Cov.: 32 AF XY: 0.261 AC XY: 19391 AN XY: 74300

African (AFR) AF: 0.179 AC: 7421 AN: 41466

American (AMR) AF: 0.254 AC: 3878 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1703 AN: 5176

South Asian (SAS) AF: 0.209 AC: 1007 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4236 AN: 10524

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.283 AC: 19236 AN: 67970

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.253 Hom.: 953

Bravo AF: 0.241

Asia WGS AF: 0.269 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.56
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs9550855; hg19: chr13-23236792;