rs10980510

chr9-110660139-A-G

Variant summary

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

The variant allele was found at a frequency of 0.109 in 152,020 control chromosomes in the GnomAD database, including 976 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 0.11 (976 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 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

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16597 AN: 151902 Hom.: 975 Cov.: 30

Gnomad AFR AF: 0.0733

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.109 AC: 16602 AN: 152020 Hom.: 976 Cov.: 30 AF XY: 0.111 AC XY: 8268 AN XY: 74268

Gnomad4 AFR AF: 0.0733

Gnomad4 AMR AF: 0.0919

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.117

Alfa AF: 0.107 Hom.: 384

Bravo AF: 0.104

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.3
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10980510; hg19: chr9-113422419;