rs9405112

Variant names:

• chr6-32477823-G-A
• rs9405112
• ENST00000829864.1:n.273+3614G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32477823-G-A
• chr6-32477823-G-T

Variant summary

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

The ENST00000829864.1(ENSG00000307923):​n.273+3614G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,072 control chromosomes in the GnomAD database, including 6,802 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 0.29 (6802 hom., cov: 35)
• Consequence: ENSG00000307923 ENST00000829864.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975
• Publications: 19 publications found

Genes affected

ENSG00000307923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 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
ENSG00000307923	ENST00000829864.1	n.273+3614G>A		intron_variant	Intron 2 of 2
ENSG00000307923	ENST00000829865.1	n.270-1313G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44140 AN: 151954 Hom.: 6801 Cov.: 35

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.290 AC: 44167 AN: 152072 Hom.: 6802 Cov.: 35 AF XY: 0.286 AC XY: 21288 AN XY: 74320

African (AFR) AF: 0.226 AC: 9372 AN: 41482

American (AMR) AF: 0.358 AC: 5469 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1776 AN: 5184

South Asian (SAS) AF: 0.258 AC: 1242 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2484 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21202 AN: 67962

Other (OTH) AF: 0.304 AC: 639 AN: 2104

Alfa AF: 0.0964 Hom.: 113

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs9405112; hg19: chr6-32445600;