rs28477715

Variant names:

• chr1-241977539-T-C
• rs28477715

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 0.107 in 151,986 control chromosomes in the GnomAD database, including 1,003 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 0.11 (1003 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16283 AN: 151870 Hom.: 999 Cov.: 31

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.0974

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0627

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.107 AC: 16300 AN: 151986 Hom.: 1003 Cov.: 31 AF XY: 0.102 AC XY: 7606 AN XY: 74284

African (AFR) AF: 0.0531 AC: 2202 AN: 41458

American (AMR) AF: 0.0823 AC: 1255 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0974 AC: 338 AN: 3472

East Asian (EAS) AF: 0.0816 AC: 421 AN: 5158

South Asian (SAS) AF: 0.0632 AC: 304 AN: 4812

European-Finnish (FIN) AF: 0.0994 AC: 1050 AN: 10562

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10301 AN: 67954

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.136 Hom.: 2001

Bravo AF: 0.105

Asia WGS AF: 0.0730 AC: 254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.95
DANN	Benign	0.40
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs28477715; hg19: chr1-242140841;