rs10183984

Variant names:

• chr2-166616406-A-G
• rs10183984

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 0.106 in 152,228 control chromosomes in the GnomAD database, including 1,045 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 (1045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 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: 0.106 AC: 16175 AN: 152110 Hom.: 1044 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.106 AC: 16192 AN: 152228 Hom.: 1045 Cov.: 32 AF XY: 0.104 AC XY: 7762 AN XY: 74440

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.109

Alfa AF: 0.105 Hom.: 1153

Bravo AF: 0.108

Asia WGS AF: 0.107 AC: 370 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10183984; hg19: chr2-167472916;