rs10987845

chr9-128039877-G-Achr9-128039877-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414976.1(ENSG00000230848):n.208-570C>T variant causes a intron, non coding transcript 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: ENST00000414976.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000414976.1	n.208-570C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.205

Alfa AF: 0.166 Hom.: 1496

Bravo AF: 0.216

Asia WGS AF: 0.209 AC: 726 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	1.1
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10987845; hg19: chr9-130802156;