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: 124 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.

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: 0.190 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

Significance: drug response

Submissions summary: Other:1

Revision: reviewed by expert panel

Submissions by phenotype

warfarin response - Dosage Other:1

Apr 12, 2021

PharmGKB

Significance: drug response

Review Status: reviewed by expert panel

Collection Method: curation

PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance. Drug-variant association: Dosage

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs12777823; hg19: chr10-96405502;