1-218821931-C-T

Variant names:

• chr1-218821931-C-T
• rs7552186

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 0.392 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.523 AC: 21662 AN: 41428

American (AMR) AF: 0.314 AC: 4790 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3468

East Asian (EAS) AF: 0.134 AC: 692 AN: 5174

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4816

European-Finnish (FIN) AF: 0.405 AC: 4281 AN: 10560

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24329 AN: 67930

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.126 Hom.: 613

Bravo AF: 0.392

Asia WGS AF: 0.212 AC: 739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.55
DANN	Benign	0.46
PhyloP100		-1.1

Splicing

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

Other links and lift over

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