1-79800243-A-G

Variant names:

• chr1-79800243-A-G
• rs10493647

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 0.939 in 152,276 control chromosomes in the GnomAD database, including 67,448 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 0.94 (67448 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 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: 0.939 AC: 142911 AN: 152158 Hom.: 67399 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.986

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.959

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.939 AC: 143016 AN: 152276 Hom.: 67448 Cov.: 32 AF XY: 0.940 AC XY: 70011 AN XY: 74442

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.986

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.959

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.942

Alfa AF: 0.959 Hom.: 8710

Bravo AF: 0.933

Asia WGS AF: 0.947 AC: 3295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493647; hg19: chr1-80265928;