rs1880670

Variant names:

• chr1-109398511-C-T
• rs1880670

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 0.647 in 152,030 control chromosomes in the GnomAD database, including 33,699 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 (33699 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 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: 0.647 AC: 98336 AN: 151912 Hom.: 33680 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.647 AC: 98374 AN: 152030 Hom.: 33699 Cov.: 32 AF XY: 0.651 AC XY: 48408 AN XY: 74304

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.700

Alfa AF: 0.654 Hom.: 4890

Bravo AF: 0.647

Asia WGS AF: 0.796 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880670; hg19: chr1-109941133;