rs1473527

Variant names:

• chr1-218448977-G-A
• rs1473527

Your query was ambiguous. Multiple possible variants found:

• chr1-218448977-G-A
• chr1-218448977-G-T

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 0.411 in 152,000 control chromosomes in the GnomAD database, including 14,455 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 0.41 (14455 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.411 AC: 62351 AN: 151882 Hom.: 14418 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.411 AC: 62441 AN: 152000 Hom.: 14455 Cov.: 32 AF XY: 0.415 AC XY: 30821 AN XY: 74294

African (AFR) AF: 0.586 AC: 24250 AN: 41416

American (AMR) AF: 0.489 AC: 7478 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3787 AN: 5168

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3387 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19370 AN: 67960

Other (OTH) AF: 0.394 AC: 830 AN: 2108

Alfa AF: 0.325 Hom.: 9725

Bravo AF: 0.435

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.022
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1473527; hg19: chr1-218622319;