rs669764

Variant names:

• chr1-78225976-C-T
• rs669764

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 0.431 in 151,784 control chromosomes in the GnomAD database, including 15,408 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 0.43 (15408 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

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 (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.431 AC: 65360 AN: 151664 Hom.: 15383 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.431 AC: 65436 AN: 151784 Hom.: 15408 Cov.: 32 AF XY: 0.436 AC XY: 32306 AN XY: 74166

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.432

Alfa AF: 0.348 Hom.: 19540

Bravo AF: 0.444

Asia WGS AF: 0.504 AC: 1755 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	1.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs669764; hg19: chr1-78691660;