rs13209234

Variant names:

• chr6-32448198-G-A
• rs13209234
• ENST00000766007.1:n.163-9938C>T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.163-9938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 151,932 control chromosomes in the GnomAD database, including 1,415 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 0.13 (1415 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 30 publications found

Genes affected

ENSG00000299747 (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 (NFE) allele frequency at 95% confidence interval = 0.146 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
ENSG00000299747	ENST00000766007.1	n.163-9938C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19296 AN: 151818 Hom.: 1415 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0618

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.127 AC: 19314 AN: 151932 Hom.: 1415 Cov.: 32 AF XY: 0.131 AC XY: 9690 AN XY: 74236

African (AFR) AF: 0.0849 AC: 3515 AN: 41408

American (AMR) AF: 0.108 AC: 1644 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0618 AC: 214 AN: 3462

East Asian (EAS) AF: 0.0426 AC: 220 AN: 5170

South Asian (SAS) AF: 0.141 AC: 679 AN: 4812

European-Finnish (FIN) AF: 0.220 AC: 2309 AN: 10508

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10099 AN: 67964

Other (OTH) AF: 0.123 AC: 260 AN: 2110

Alfa AF: 0.134 Hom.: 4112

Bravo AF: 0.117

Asia WGS AF: 0.0970 AC: 343 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	0.39
DANN	Benign	0.30
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13209234; hg19: chr6-32415975;