rs3000140

Positions:

• chr1-79534963-G-T

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 0.0803 in 152,008 control chromosomes in the GnomAD database, including 1,257 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 0.080 (1257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.802

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12173 AN: 151890 Hom.: 1250 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.00375

Gnomad EAS AF: 0.0533

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0144

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0803 AC: 12207 AN: 152008 Hom.: 1257 Cov.: 32 AF XY: 0.0787 AC XY: 5847 AN XY: 74308

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.00375

Gnomad4 EAS AF: 0.0530

Gnomad4 SAS AF: 0.0640

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0144

Gnomad4 OTH AF: 0.0579

Alfa AF: 0.0512 Hom.: 179

Bravo AF: 0.0872

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3000140; hg19: chr1-80000648;