chr1-5294784-C-T

Variant names:

• chr1-5294784-C-T
• rs912988

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 0.319 in 152,048 control chromosomes in the GnomAD database, including 8,270 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 0.32 (8270 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.319 AC: 48422 AN: 151930 Hom.: 8271 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.319 AC: 48434 AN: 152048 Hom.: 8270 Cov.: 32 AF XY: 0.319 AC XY: 23712 AN XY: 74330

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.330

Alfa AF: 0.362 Hom.: 13795

Bravo AF: 0.306

Asia WGS AF: 0.192 AC: 669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs912988; hg19: chr1-5354844;