chr1-218240701-T-G

Position:

• chr1-218240701-T-G

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 0.654 in 152,068 control chromosomes in the GnomAD database, including 33,100 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 0.65 (33100 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

(HGNC:):

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 = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.218240701T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99378 AN: 151950 Hom.: 33042 Cov.: 33

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.654 AC: 99491 AN: 152068 Hom.: 33100 Cov.: 33 AF XY: 0.657 AC XY: 48862 AN XY: 74342

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.678

Alfa AF: 0.616 Hom.: 13239

Bravo AF: 0.675

Asia WGS AF: 0.817 AC: 2839 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	0.049
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6663771; hg19: chr1-218414043; COSMIC: COSV60028052;