1-218821931-C-T

Variant names:

• chr1-218821931-C-T
• rs7552186

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 0.392 in 151,948 control chromosomes in the GnomAD database, including 12,423 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 0.39 (12423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 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: 0.392 AC: 59452 AN: 151830 Hom.: 12407 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.392 AC: 59522 AN: 151948 Hom.: 12423 Cov.: 32 AF XY: 0.387 AC XY: 28766 AN XY: 74278

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.373

Alfa AF: 0.258 Hom.: 613

Bravo AF: 0.392

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.55
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7552186; hg19: chr1-218995273; COSMIC: COSV67738402;