rs12777823

Variant names:

• chr10-94645745-G-A
• rs12777823

Your query was ambiguous. Multiple possible variants found:

• chr10-94645745-G-A
• chr10-94645745-G-T

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 0.19 in 152,074 control chromosomes in the GnomAD database, including 3,069 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).

• Frequency: Genomes: 𝑓 0.19 (3069 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: drug response reviewed by expert panel O:1
• Conservation: PhyloP100: 0.0780
• Publications: 128 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.190 AC: 28938 AN: 151956 Hom.: 3063 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.190 AC: 28965 AN: 152074 Hom.: 3069 Cov.: 33 AF XY: 0.194 AC XY: 14442 AN XY: 74320

African (AFR) AF: 0.250 AC: 10354 AN: 41478

American (AMR) AF: 0.140 AC: 2146 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1614 AN: 5174

South Asian (SAS) AF: 0.335 AC: 1611 AN: 4816

European-Finnish (FIN) AF: 0.184 AC: 1941 AN: 10562

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10288 AN: 67978

Other (OTH) AF: 0.169 AC: 358 AN: 2114

Alfa AF: 0.166 Hom.: 6956

Bravo AF: 0.185

Asia WGS AF: 0.311 AC: 1079 AN: 3478

ClinVar

ClinVar submissions

Significance: drug response

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	-	-	warfarin response - Dosage (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.8
DANN	Benign	0.26
PhyloP100		0.078

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12777823; hg19: chr10-96405502;