rs2394534

Variant names:

• chr10-69269546-T-G
• rs2394534

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 0.181 in 152,260 control chromosomes in the GnomAD database, including 2,993 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 0.18 (2993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 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: 0.181 AC: 27596 AN: 152142 Hom.: 2995 Cov.: 32

Gnomad AFR AF: 0.0792

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.181 AC: 27595 AN: 152260 Hom.: 2993 Cov.: 32 AF XY: 0.183 AC XY: 13590 AN XY: 74448

African (AFR) AF: 0.0791 AC: 3288 AN: 41552

American (AMR) AF: 0.193 AC: 2956 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3468

East Asian (EAS) AF: 0.0784 AC: 407 AN: 5190

South Asian (SAS) AF: 0.199 AC: 962 AN: 4834

European-Finnish (FIN) AF: 0.261 AC: 2770 AN: 10596

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16141 AN: 68008

Other (OTH) AF: 0.164 AC: 345 AN: 2108

Alfa AF: 0.207 Hom.: 5224

Bravo AF: 0.169

Asia WGS AF: 0.131 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.7
DANN	Benign	0.73
PhyloP100		-0.54
PromoterAI		-0.0058	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2394534; hg19: chr10-71029302;