1-111033299-T-G

Variant names:

• chr1-111033299-T-G
• rs1578790

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 0.546 in 151,914 control chromosomes in the GnomAD database, including 22,931 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 0.55 (22931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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: 0.546 AC: 82833 AN: 151796 Hom.: 22920 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.546 AC: 82874 AN: 151914 Hom.: 22931 Cov.: 31 AF XY: 0.537 AC XY: 39849 AN XY: 74264

African (AFR) AF: 0.587 AC: 24283 AN: 41390

American (AMR) AF: 0.530 AC: 8086 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2139 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1671 AN: 5166

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4818

European-Finnish (FIN) AF: 0.496 AC: 5227 AN: 10546

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.556 AC: 37777 AN: 67952

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.555 Hom.: 73572

Bravo AF: 0.553

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.71
DANN	Benign	0.62
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1578790; hg19: chr1-111575921;