1-47193020-C-G

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 0.773 in 152,106 control chromosomes in the GnomAD database, including 45,986 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 0.77 (45986 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.733

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 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: 0.773 AC: 117561 AN: 151988 Hom.: 45947 Cov.: 31

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.773 AC: 117643 AN: 152106 Hom.: 45986 Cov.: 31 AF XY: 0.770 AC XY: 57205 AN XY: 74334

Gnomad4 AFR AF: 0.861

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.771

Alfa AF: 0.709 Hom.: 2090

Bravo AF: 0.775

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.9
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941412; hg19: chr1-47658692;