rs1159268

Positions:

• chr1-218671564-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.317

Alfa AF: 0.327 Hom.: 3777

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1159268; hg19: chr1-218844906;