rs1159268

Variant names:

• chr1-218671564-G-A
• rs1159268

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 0.326 in 151,918 control chromosomes in the GnomAD database, including 8,280 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 0.33 (8280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.326 AC: 49493 AN: 151798 Hom.: 8274 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.326 AC: 49522 AN: 151918 Hom.: 8280 Cov.: 32 AF XY: 0.323 AC XY: 24012 AN XY: 74238

African (AFR) AF: 0.320 AC: 13252 AN: 41424

American (AMR) AF: 0.300 AC: 4584 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 906 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2632 AN: 5154

South Asian (SAS) AF: 0.298 AC: 1434 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3113 AN: 10548

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22654 AN: 67944

Other (OTH) AF: 0.317 AC: 666 AN: 2104

Alfa AF: 0.340 Hom.: 16945

Bravo AF: 0.329

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1159268; hg19: chr1-218844906;