chr13-40028210-C-T

Variant names:

• chr13-40028210-C-T
• rs9603665
• ENST00000837163.1:n.167+13195G>A

Variant summary

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

The ENST00000837163.1(ENSG00000308901):​n.167+13195G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,048 control chromosomes in the GnomAD database, including 7,697 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 0.30 (7697 hom., cov: 31)
• Consequence: ENSG00000308901 ENST00000837163.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 2 publications found

Genes affected

ENSG00000308901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 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
ENSG00000308901	ENST00000837163.1	n.167+13195G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46185 AN: 151930 Hom.: 7695 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.304 AC: 46190 AN: 152048 Hom.: 7697 Cov.: 31 AF XY: 0.301 AC XY: 22398 AN XY: 74328

African (AFR) AF: 0.177 AC: 7335 AN: 41504

American (AMR) AF: 0.394 AC: 6022 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 989 AN: 3470

East Asian (EAS) AF: 0.187 AC: 963 AN: 5162

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4822

European-Finnish (FIN) AF: 0.352 AC: 3716 AN: 10548

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25014 AN: 67940

Other (OTH) AF: 0.292 AC: 616 AN: 2106

Alfa AF: 0.347 Hom.: 16039

Bravo AF: 0.305

Asia WGS AF: 0.195 AC: 678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.23
DANN	Benign	0.53
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs9603665; hg19: chr13-40602347;