chr1-12164396-A-G

Position:

• chr1-12164396-A-G

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 0.161 in 151,920 control chromosomes in the GnomAD database, including 4,670 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 0.16 (4670 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24456 AN: 151802 Hom.: 4654 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0445

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0462

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.161 AC: 24534 AN: 151920 Hom.: 4670 Cov.: 32 AF XY: 0.155 AC XY: 11472 AN XY: 74252

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0445

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0253

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0462

Gnomad4 OTH AF: 0.140

Alfa AF: 0.153 Hom.: 635

Bravo AF: 0.179

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.015
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs520916; hg19: chr1-12224453; COSMIC: COSV66163600;