chr1-229435314-T-G

Variant names:

• chr1-229435314-T-G
• rs506388

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 152,104 control chromosomes in the GnomAD database, including 28,623 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 (28623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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: 92730 AN: 151986 Hom.: 28591 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.610 AC: 92813 AN: 152104 Hom.: 28623 Cov.: 32 AF XY: 0.606 AC XY: 45089 AN XY: 74374

African (AFR) AF: 0.676 AC: 28057 AN: 41496

American (AMR) AF: 0.647 AC: 9888 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2525 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2476 AN: 5174

South Asian (SAS) AF: 0.659 AC: 3179 AN: 4822

European-Finnish (FIN) AF: 0.478 AC: 5063 AN: 10582

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39482 AN: 67954

Other (OTH) AF: 0.640 AC: 1352 AN: 2112

Alfa AF: 0.597 Hom.: 113970

Bravo AF: 0.625

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	17
DANN	Benign	0.83
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs506388; hg19: chr1-229571061;