chr13-37215773-T-C

Variant names:

• chr13-37215773-T-C
• rs9576222
• ENST00000827668.1:n.232+60049T>C

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.232+60049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 150,590 control chromosomes in the GnomAD database, including 5,428 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 0.24 (5428 hom., cov: 26)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267
• Publications: 3 publications found

Genes affected

ENSG00000307651 (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 (EAS) allele frequency at 95% confidence interval = 0.751 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
ENSG00000307651	ENST00000827668.1	n.232+60049T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36029 AN: 150470 Hom.: 5426 Cov.: 26

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.219

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.239 AC: 36026 AN: 150590 Hom.: 5428 Cov.: 26 AF XY: 0.248 AC XY: 18246 AN XY: 73464

African (AFR) AF: 0.119 AC: 4873 AN: 41040

American (AMR) AF: 0.289 AC: 4359 AN: 15100

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 712 AN: 3462

East Asian (EAS) AF: 0.771 AC: 3863 AN: 5010

South Asian (SAS) AF: 0.289 AC: 1377 AN: 4760

European-Finnish (FIN) AF: 0.374 AC: 3834 AN: 10238

Middle Eastern (MID) AF: 0.215 AC: 62 AN: 288

European-Non Finnish (NFE) AF: 0.238 AC: 16086 AN: 67700

Other (OTH) AF: 0.245 AC: 511 AN: 2084

Alfa AF: 0.226 Hom.: 731

Bravo AF: 0.231

Asia WGS AF: 0.506 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.58
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs9576222; hg19: chr13-37789910;