1-27077270-T-C

Variant names:

• chr1-27077270-T-C
• rs484677

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 0.622 in 151,938 control chromosomes in the GnomAD database, including 29,971 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 0.62 (29971 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.622 AC: 94451 AN: 151820 Hom.: 29953 Cov.: 31

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.622 AC: 94519 AN: 151938 Hom.: 29971 Cov.: 31 AF XY: 0.629 AC XY: 46663 AN XY: 74240

African (AFR) AF: 0.602 AC: 24923 AN: 41432

American (AMR) AF: 0.743 AC: 11308 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2063 AN: 3466

East Asian (EAS) AF: 0.913 AC: 4727 AN: 5180

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4816

European-Finnish (FIN) AF: 0.600 AC: 6332 AN: 10550

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39522 AN: 67960

Other (OTH) AF: 0.668 AC: 1409 AN: 2110

Alfa AF: 0.604 Hom.: 46407

Bravo AF: 0.633

Asia WGS AF: 0.782 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.28
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs484677; hg19: chr1-27403761;