rs10980510

Variant names:

• chr9-110660139-A-G
• rs10980510

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;