chr1-67303323-A-G

Position:

• chr1-67303323-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.653

Alfa AF: 0.737 Hom.: 54891

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12131065; hg19: chr1-67769006;