rs10183984

Positions:

• chr2-166616406-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 0.106 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;