rs10983755

Variant names:

• chr9-117702392-G-A
• rs10983755

Variant summary

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

The variant allele was found at a frequency of 0.0353 in 152,242 control chromosomes in the GnomAD database, including 237 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 0.035 (237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 62 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0353 AC: 5365 AN: 152124 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0126

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0624

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0353 AC: 5367 AN: 152242 Hom.: 237 Cov.: 32 AF XY: 0.0386 AC XY: 2870 AN XY: 74434

African (AFR) AF: 0.0126 AC: 523 AN: 41554

American (AMR) AF: 0.0220 AC: 337 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.236 AC: 1218 AN: 5162

South Asian (SAS) AF: 0.0780 AC: 376 AN: 4822

European-Finnish (FIN) AF: 0.0624 AC: 661 AN: 10592

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0299 AC: 2033 AN: 68024

Other (OTH) AF: 0.0327 AC: 69 AN: 2112

Alfa AF: 0.0294 Hom.: 45

Bravo AF: 0.0332

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10983755; hg19: chr9-120464670;