rs1328657

Variant names:

• chr13-97531632-C-T
• rs1328657
• ENST00000802609.1:n.308+15479G>A

Variant summary

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

The ENST00000802609.1(ENSG00000304344):​n.308+15479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,064 control chromosomes in the GnomAD database, including 5,099 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 0.23 (5099 hom., cov: 32)
• Consequence: ENSG00000304344 ENST00000802609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 2 publications found

Genes affected

ENSG00000304344 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370324	XR_007063845.1	n.*122G>A		downstream_gene_variant
LOC105370324	XR_931663.3	n.*122G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304344	ENST00000802609.1	n.308+15479G>A		intron_variant	Intron 2 of 2
ENSG00000304344	ENST00000802610.1	n.375+15479G>A		intron_variant	Intron 3 of 3
ENSG00000304344	ENST00000802611.1	n.711+1854G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35210 AN: 151946 Hom.: 5101 Cov.: 32

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.232 AC: 35207 AN: 152064 Hom.: 5099 Cov.: 32 AF XY: 0.239 AC XY: 17722 AN XY: 74300

African (AFR) AF: 0.0554 AC: 2302 AN: 41520

American (AMR) AF: 0.304 AC: 4636 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 965 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1263 AN: 5162

South Asian (SAS) AF: 0.393 AC: 1891 AN: 4814

European-Finnish (FIN) AF: 0.342 AC: 3614 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19631 AN: 67968

Other (OTH) AF: 0.255 AC: 537 AN: 2104

Alfa AF: 0.287 Hom.: 9293

Bravo AF: 0.220

Asia WGS AF: 0.273 AC: 950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.83
DANN	Benign	0.73
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1328657; hg19: chr13-98183886;