chr9-128039877-G-A

Variant names:

• chr9-128039877-G-A
• rs10987845
• ENST00000414976.2:n.308-570C>T

Variant summary

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

The ENST00000414976.2(ENSG00000230848):​n.308-570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 148,042 control chromosomes in the GnomAD database, including 3,702 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 0.21 (3702 hom., cov: 28)
• Consequence: ENSG00000230848 ENST00000414976.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 7 publications found

Genes affected

ENSG00000230848 (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 (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414976.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230848	ENST00000414976.2	TSL:3	n.308-570C>T		intron	N/A
	ENSG00000230848	ENST00000839691.1		n.307+17279C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.213 AC: 31525 AN: 147930 Hom.: 3697 Cov.: 28

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.213 AC: 31565 AN: 148042 Hom.: 3702 Cov.: 28 AF XY: 0.213 AC XY: 15299 AN XY: 71784

African (AFR) AF: 0.326 AC: 13125 AN: 40312

American (AMR) AF: 0.190 AC: 2735 AN: 14392

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 688 AN: 3450

East Asian (EAS) AF: 0.131 AC: 654 AN: 5006

South Asian (SAS) AF: 0.271 AC: 1276 AN: 4710

European-Finnish (FIN) AF: 0.151 AC: 1438 AN: 9546

Middle Eastern (MID) AF: 0.197 AC: 52 AN: 264

European-Non Finnish (NFE) AF: 0.163 AC: 11010 AN: 67422

Other (OTH) AF: 0.205 AC: 417 AN: 2036

Alfa AF: 0.171 Hom.: 2468

Bravo AF: 0.216

Asia WGS AF: 0.209 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs10987845; hg19: chr9-130802156;