1-237935790-T-G

Variant names:

• chr1-237935790-T-G
• rs693421

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 0.61 in 152,042 control chromosomes in the GnomAD database, including 28,531 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 0.61 (28531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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: 0.610 AC: 92667 AN: 151922 Hom.: 28506 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.610 AC: 92741 AN: 152042 Hom.: 28531 Cov.: 32 AF XY: 0.611 AC XY: 45420 AN XY: 74292

African (AFR) AF: 0.697 AC: 28899 AN: 41488

American (AMR) AF: 0.564 AC: 8609 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2180 AN: 3470

East Asian (EAS) AF: 0.516 AC: 2663 AN: 5164

South Asian (SAS) AF: 0.605 AC: 2916 AN: 4818

European-Finnish (FIN) AF: 0.593 AC: 6256 AN: 10554

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39208 AN: 67976

Other (OTH) AF: 0.606 AC: 1279 AN: 2110

Alfa AF: 0.579 Hom.: 9856

Bravo AF: 0.608

Asia WGS AF: 0.611 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs693421; hg19: chr1-238099090;