9-113659996-A-G

Variant names:

• chr9-113659996-A-G
• rs10981870
• ENST00000428292.1:n.273+7916A>G

Variant summary

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

The ENST00000428292.1(ENSG00000227482):​n.273+7916A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,058 control chromosomes in the GnomAD database, including 6,924 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 0.30 (6924 hom., cov: 32)
• Consequence: ENSG00000227482 ENST00000428292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

Genes affected

ENSG00000227482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376223	XR_930254.3	n.192+7916A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227482	ENST00000428292.1	n.273+7916A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44918 AN: 151940 Hom.: 6903 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.296 AC: 44979 AN: 152058 Hom.: 6924 Cov.: 32 AF XY: 0.289 AC XY: 21475 AN XY: 74322

African (AFR) AF: 0.309 AC: 12822 AN: 41466

American (AMR) AF: 0.259 AC: 3964 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.110 AC: 568 AN: 5162

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4818

European-Finnish (FIN) AF: 0.209 AC: 2205 AN: 10572

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21875 AN: 67960

Other (OTH) AF: 0.306 AC: 648 AN: 2116

Alfa AF: 0.295 Hom.: 1193

Bravo AF: 0.298

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.69
PhyloP100		0.31

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10981870; hg19: chr9-116422276;