chr1-30319365-G-A

Variant names:

• chr1-30319365-G-A
• rs437709

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 0.333 in 152,016 control chromosomes in the GnomAD database, including 10,710 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 0.33 (10710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50517 AN: 151898 Hom.: 10698 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.333 AC: 50553 AN: 152016 Hom.: 10710 Cov.: 32 AF XY: 0.325 AC XY: 24141 AN XY: 74300

African (AFR) AF: 0.597 AC: 24745 AN: 41426

American (AMR) AF: 0.196 AC: 2993 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 678 AN: 3472

East Asian (EAS) AF: 0.0504 AC: 260 AN: 5158

South Asian (SAS) AF: 0.106 AC: 513 AN: 4822

European-Finnish (FIN) AF: 0.263 AC: 2788 AN: 10586

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17841 AN: 67954

Other (OTH) AF: 0.271 AC: 572 AN: 2112

Alfa AF: 0.291 Hom.: 1412

Bravo AF: 0.340

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.010
DANN	Benign	0.74
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs437709; hg19: chr1-30792212; COSMIC: COSV59935315;