chr1-218758563-G-T

Variant names:

• chr1-218758563-G-T
• rs12037343

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 0.0641 in 152,238 control chromosomes in the GnomAD database, including 708 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 0.064 (708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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: 0.0642 AC: 9765 AN: 152120 Hom.: 709 Cov.: 33

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0815

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0641 AC: 9766 AN: 152238 Hom.: 708 Cov.: 33 AF XY: 0.0678 AC XY: 5048 AN XY: 74440

African (AFR) AF: 0.0306 AC: 1270 AN: 41568

American (AMR) AF: 0.0819 AC: 1253 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 272 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2097 AN: 5156

South Asian (SAS) AF: 0.141 AC: 679 AN: 4820

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10606

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0505 AC: 3434 AN: 68002

Other (OTH) AF: 0.0936 AC: 198 AN: 2116

Alfa AF: 0.0768 Hom.: 332

Bravo AF: 0.0670

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs12037343; hg19: chr1-218931905;