1-78704323-G-C

Variant names:

• chr1-78704323-G-C
• rs6424785

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 0.476 in 152,122 control chromosomes in the GnomAD database, including 17,468 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 0.48 (17468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.476 AC: 72285 AN: 152004 Hom.: 17449 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.450

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.476 AC: 72336 AN: 152122 Hom.: 17468 Cov.: 32 AF XY: 0.480 AC XY: 35674 AN XY: 74358

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.450

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.504

Alfa AF: 0.478 Hom.: 2294

Bravo AF: 0.486

Asia WGS AF: 0.534 AC: 1858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.043
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: rs6424785; hg19: chr1-79170008;