chr1-114310885-G-C

Variant names:

• chr1-114310885-G-C
• rs12711445

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 0.776 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.496 AC: 20594 AN: 41488

American (AMR) AF: 0.835 AC: 12767 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3003 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5186 AN: 5190

South Asian (SAS) AF: 0.924 AC: 4455 AN: 4820

European-Finnish (FIN) AF: 0.918 AC: 9745 AN: 10618

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59536 AN: 67994

Other (OTH) AF: 0.791 AC: 1669 AN: 2110

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

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