rs12063780

Variant names:

• chr1-207101949-C-G
• rs12063780

Your query was ambiguous. Multiple possible variants found:

• chr1-207101949-C-G
• chr1-207101949-C-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 0.135 in 152,154 control chromosomes in the GnomAD database, including 1,985 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 0.14 (1985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.135 AC: 20573 AN: 152036 Hom.: 1978 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0898

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0699

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.135 AC: 20605 AN: 152154 Hom.: 1985 Cov.: 32 AF XY: 0.134 AC XY: 9935 AN XY: 74374

African (AFR) AF: 0.273 AC: 11333 AN: 41468

American (AMR) AF: 0.0898 AC: 1373 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.201 AC: 1041 AN: 5178

South Asian (SAS) AF: 0.130 AC: 625 AN: 4822

European-Finnish (FIN) AF: 0.0599 AC: 634 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0699 AC: 4751 AN: 68016

Other (OTH) AF: 0.142 AC: 301 AN: 2114

Alfa AF: 0.103 Hom.: 156

Bravo AF: 0.143

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs12063780; hg19: chr1-207275294;