chr1-111043892-T-C

Variant names:

• chr1-111043892-T-C
• rs1774778

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 0.558 in 151,964 control chromosomes in the GnomAD database, including 23,992 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 0.56 (23992 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.558 AC: 84782 AN: 151846 Hom.: 23981 Cov.: 31

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.558 AC: 84819 AN: 151964 Hom.: 23992 Cov.: 31 AF XY: 0.549 AC XY: 40793 AN XY: 74276

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.565

Gnomad4 OTH AF: 0.549

Alfa AF: 0.564 Hom.: 3006

Bravo AF: 0.565

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.8
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1774778; hg19: chr1-111586514;