rs780240

Variant names:

• chr1-233544817-C-T
• rs780240

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 0.686 in 151,626 control chromosomes in the GnomAD database, including 35,963 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 0.69 (35963 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

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 (SAS) allele frequency at 95% confidence interval = 0.75 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: 0.686 AC: 103946 AN: 151510 Hom.: 35927 Cov.: 28

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.686 AC: 104023 AN: 151626 Hom.: 35963 Cov.: 28 AF XY: 0.685 AC XY: 50741 AN XY: 74074

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.680

Alfa AF: 0.692 Hom.: 50780

Bravo AF: 0.667

Asia WGS AF: 0.718 AC: 2496 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	1.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs780240; hg19: chr1-233680563;