1-219627563-T-C

Position:

• chr1-219627563-T-C

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 0.759 in 152,004 control chromosomes in the GnomAD database, including 44,729 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 0.76 (44729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.83

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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: 0.759 AC: 115254 AN: 151886 Hom.: 44708 Cov.: 32

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.759 AC: 115321 AN: 152004 Hom.: 44729 Cov.: 32 AF XY: 0.762 AC XY: 56635 AN XY: 74304

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.770

Alfa AF: 0.806 Hom.: 27669

Bravo AF: 0.747

Asia WGS AF: 0.874 AC: 3042 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.016
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1338221; hg19: chr1-219800905;