1-67303323-A-G

Variant names:

• chr1-67303323-A-G
• rs12131065

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 0.649 in 151,616 control chromosomes in the GnomAD database, including 33,960 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 0.65 (33960 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 11 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 (NFE) allele frequency at 95% confidence interval = 0.759 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: 0.649 AC: 98265 AN: 151516 Hom.: 33939 Cov.: 30

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.649 AC: 98327 AN: 151616 Hom.: 33960 Cov.: 30 AF XY: 0.649 AC XY: 48080 AN XY: 74058

African (AFR) AF: 0.395 AC: 16310 AN: 41284

American (AMR) AF: 0.677 AC: 10314 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2771 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3170 AN: 5144

South Asian (SAS) AF: 0.697 AC: 3352 AN: 4808

European-Finnish (FIN) AF: 0.790 AC: 8233 AN: 10418

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.765 AC: 51948 AN: 67942

Other (OTH) AF: 0.653 AC: 1377 AN: 2110

Alfa AF: 0.719 Hom.: 85274

Bravo AF: 0.631

Asia WGS AF: 0.619 AC: 2153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs12131065; hg19: chr1-67769006;