1-79534963-G-T

Variant names:

• chr1-79534963-G-T
• rs3000140

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;