1-79725181-G-C

Variant names:

• chr1-79725181-G-C
• rs6424669

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 0.915 in 152,002 control chromosomes in the GnomAD database, including 64,025 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 0.92 (64025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 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: 0.915 AC: 138985 AN: 151884 Hom.: 63979 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.915 AC: 139088 AN: 152002 Hom.: 64025 Cov.: 32 AF XY: 0.915 AC XY: 67954 AN XY: 74284

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.945

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.962

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.914

Alfa AF: 0.944 Hom.: 3260

Bravo AF: 0.910

Asia WGS AF: 0.905 AC: 3141 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6424669; hg19: chr1-80190866;