rs28757217

Variant names:

• chr1-163064226-G-A
• rs28757217

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 0.0492 in 152,106 control chromosomes in the GnomAD database, including 222 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 0.049 (222 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.053 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: 0.0492 AC: 7474 AN: 151988 Hom.: 222 Cov.: 32

Gnomad AFR AF: 0.0320

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0560

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0722

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.0642

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

GnomAD4 genome AF: 0.0492 AC: 7483 AN: 152106 Hom.: 222 Cov.: 32 AF XY: 0.0500 AC XY: 3718 AN XY: 74346

African (AFR) AF: 0.0320 AC: 1330 AN: 41510

American (AMR) AF: 0.0561 AC: 857 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.0550 AC: 284 AN: 5166

South Asian (SAS) AF: 0.0432 AC: 208 AN: 4814

European-Finnish (FIN) AF: 0.0722 AC: 764 AN: 10578

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0509 AC: 3461 AN: 67986

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0255 Hom.: 13

Bravo AF: 0.0471

Asia WGS AF: 0.0510 AC: 177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.38
DANN	Benign	0.63
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs28757217; hg19: chr1-163034016;