rs10429616

Variant names:

• chr9-115756454-A-G
• rs10429616
• ENST00000832032.1:n.322-14892T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-115756454-A-G
• chr9-115756454-A-T

Variant summary

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

The ENST00000832032.1(ENSG00000228714):​n.322-14892T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,726 control chromosomes in the GnomAD database, including 13,911 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 0.43 (13911 hom., cov: 31)
• Consequence: ENSG00000228714 ENST00000832032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 5 publications found

Genes affected

ENSG00000228714 (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 (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376234	XR_930268.2	n.367-3797A>G		intron_variant	Intron 2 of 2
LOC105376234	XR_930269.2	n.366+8728A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228714	ENST00000832032.1	n.322-14892T>C		intron_variant	Intron 1 of 2
ENSG00000308189	ENST00000832372.1	n.305+8728A>G		intron_variant	Intron 2 of 3
ENSG00000308189	ENST00000832373.1	n.334+8728A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64589 AN: 151608 Hom.: 13892 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.426 AC: 64627 AN: 151726 Hom.: 13911 Cov.: 31 AF XY: 0.423 AC XY: 31364 AN XY: 74108

African (AFR) AF: 0.454 AC: 18796 AN: 41402

American (AMR) AF: 0.340 AC: 5175 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1622 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2726 AN: 5094

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4818

European-Finnish (FIN) AF: 0.369 AC: 3889 AN: 10534

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29152 AN: 67880

Other (OTH) AF: 0.453 AC: 954 AN: 2108

Alfa AF: 0.426 Hom.: 25283

Bravo AF: 0.424

Asia WGS AF: 0.464 AC: 1610 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	0.93
DANN	Benign	0.49
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs10429616; hg19: chr9-118518733;