rs277355

chr1-74825100-T-C

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 0.43 in 151,774 control chromosomes in the GnomAD database, including 14,441 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 0.43 (14441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65232 AN: 151656 Hom.: 14430 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.430 AC: 65271 AN: 151774 Hom.: 14441 Cov.: 32 AF XY: 0.437 AC XY: 32429 AN XY: 74140

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.453

Alfa AF: 0.407 Hom.: 5947

Bravo AF: 0.428

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277355; hg19: chr1-75290784;