chr1-218448977-G-A

Position:

• chr1-218448977-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 0.411 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.394

Alfa AF: 0.324 Hom.: 7983

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1473527; hg19: chr1-218622319;