1-111114487-C-T

Variant names:

• chr1-111114487-C-T
• rs325910

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 0.249 in 152,100 control chromosomes in the GnomAD database, including 5,826 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 0.25 (5826 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.412 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: 0.248 AC: 37767 AN: 151982 Hom.: 5794 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.249 AC: 37854 AN: 152100 Hom.: 5826 Cov.: 32 AF XY: 0.253 AC XY: 18847 AN XY: 74374

African (AFR) AF: 0.418 AC: 17310 AN: 41460

American (AMR) AF: 0.266 AC: 4060 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 480 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1257 AN: 5184

South Asian (SAS) AF: 0.405 AC: 1953 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10603 AN: 67996

Other (OTH) AF: 0.251 AC: 529 AN: 2104

Alfa AF: 0.115 Hom.: 215

Bravo AF: 0.261

Asia WGS AF: 0.384 AC: 1340 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	0.54
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs325910; hg19: chr1-111657109;