1-67274409-G-A

Variant names:

• chr1-67274409-G-A
• rs11209032

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 0.303 in 152,024 control chromosomes in the GnomAD database, including 7,582 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 0.30 (7582 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 109 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 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: 0.303 AC: 45978 AN: 151904 Hom.: 7579 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.303 AC: 46017 AN: 152024 Hom.: 7582 Cov.: 33 AF XY: 0.311 AC XY: 23073 AN XY: 74302

African (AFR) AF: 0.209 AC: 8673 AN: 41496

American (AMR) AF: 0.245 AC: 3750 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1114 AN: 3470

East Asian (EAS) AF: 0.493 AC: 2548 AN: 5166

South Asian (SAS) AF: 0.538 AC: 2589 AN: 4814

European-Finnish (FIN) AF: 0.424 AC: 4469 AN: 10530

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21862 AN: 67954

Other (OTH) AF: 0.304 AC: 642 AN: 2110

Alfa AF: 0.311 Hom.: 14140

Bravo AF: 0.281

Asia WGS AF: 0.468 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.059
DANN	Benign	0.18
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11209032; hg19: chr1-67740092;