1-47193020-C-G

Variant names:

• chr1-47193020-C-G
• rs941412

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;