rs12711445

Variant names:

• chr1-114310885-G-C
• rs12711445

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 0.776 in 152,188 control chromosomes in the GnomAD database, including 48,145 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 0.78 (48145 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.776 AC: 117981 AN: 152070 Hom.: 48128 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.776 AC: 118038 AN: 152188 Hom.: 48145 Cov.: 31 AF XY: 0.783 AC XY: 58249 AN XY: 74422

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.865

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.791

Alfa AF: 0.818 Hom.: 6534

Bravo AF: 0.755

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12711445; hg19: chr1-114853507; COSMIC: COSV59989768;