rs277355

Variant names:

• chr1-74825100-T-C
• rs277355

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 0.43 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
• Publications: 1 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.405 AC: 16770 AN: 41414

American (AMR) AF: 0.454 AC: 6897 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3464

East Asian (EAS) AF: 0.766 AC: 3912 AN: 5108

South Asian (SAS) AF: 0.431 AC: 2077 AN: 4822

European-Finnish (FIN) AF: 0.503 AC: 5328 AN: 10584

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27291 AN: 67868

Other (OTH) AF: 0.453 AC: 953 AN: 2104

Alfa AF: 0.407 Hom.: 6646

Bravo AF: 0.428

Asia WGS AF: 0.582 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.60
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs277355; hg19: chr1-75290784;