rs1408229

Variant names:

• chr13-37230216-A-C
• rs1408229
• ENST00000827668.1:n.232+74492A>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+74492A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 486,974 control chromosomes in the GnomAD database, including 103,679 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 0.64 (31792 hom., cov: 31)
  • Exomes 𝑓: 0.65 (71887 hom.)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.62
• Publications: 7 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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827668.1. 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
	ENSG00000307651	ENST00000827668.1		n.232+74492A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97449 AN: 151816 Hom.: 31769 Cov.: 31

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.656

GnomAD2 exomes AF: 0.625 AC: 114267 AN: 182902 AF XY: 0.624

Gnomad AFR exome AF: 0.635

Gnomad AMR exome AF: 0.656

Gnomad ASJ exome AF: 0.701

Gnomad EAS exome AF: 0.215

Gnomad FIN exome AF: 0.600

Gnomad NFE exome AF: 0.686

Gnomad OTH exome AF: 0.660

GnomAD4 exome AF: 0.647 AC: 216690 AN: 335040 Hom.: 71887 Cov.: 0 AF XY: 0.643 AC XY: 122839 AN XY: 191042

African (AFR) AF: 0.635 AC: 6340 AN: 9988

American (AMR) AF: 0.658 AC: 20808 AN: 31636

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 7843 AN: 11168

East Asian (EAS) AF: 0.214 AC: 2595 AN: 12098

South Asian (SAS) AF: 0.600 AC: 37099 AN: 61876

European-Finnish (FIN) AF: 0.606 AC: 9142 AN: 15078

Middle Eastern (MID) AF: 0.671 AC: 1886 AN: 2810

European-Non Finnish (NFE) AF: 0.692 AC: 120956 AN: 174912

Other (OTH) AF: 0.648 AC: 10021 AN: 15474

GnomAD4 genome AF: 0.642 AC: 97508 AN: 151934 Hom.: 31792 Cov.: 31 AF XY: 0.634 AC XY: 47107 AN XY: 74266

African (AFR) AF: 0.635 AC: 26331 AN: 41436

American (AMR) AF: 0.635 AC: 9671 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2391 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1156 AN: 5170

South Asian (SAS) AF: 0.574 AC: 2765 AN: 4814

European-Finnish (FIN) AF: 0.584 AC: 6157 AN: 10548

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 47011 AN: 67950

Other (OTH) AF: 0.652 AC: 1376 AN: 2110

Alfa AF: 0.676 Hom.: 8171

Bravo AF: 0.645

Asia WGS AF: 0.425 AC: 1482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.80
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1408229; hg19: chr13-37804353; COSMIC: COSV61339060;