1-111043892-T-C

Variant names:

• chr1-111043892-T-C
• rs1774778

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 0.558 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.610 AC: 25252 AN: 41420

American (AMR) AF: 0.535 AC: 8176 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2152 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1693 AN: 5180

South Asian (SAS) AF: 0.360 AC: 1730 AN: 4806

European-Finnish (FIN) AF: 0.520 AC: 5473 AN: 10532

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38373 AN: 67968

Other (OTH) AF: 0.549 AC: 1158 AN: 2108

Alfa AF: 0.567 Hom.: 3156

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1774778; hg19: chr1-111586514;