rs277355

Variant names:

• chr1-74825100-T-C
• rs277355

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;