1-46942278-T-C

Variant names:

• chr1-46942278-T-C
• rs9332978

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0763 in 152,210 control chromosomes in the GnomAD database, including 630 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 0.076 (630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.0763 AC: 11611 AN: 152092 Hom.: 626 Cov.: 32

Gnomad AFR AF: 0.0163

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0867

Gnomad FIN AF: 0.0932

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0763 AC: 11610 AN: 152210 Hom.: 630 Cov.: 32 AF XY: 0.0796 AC XY: 5919 AN XY: 74382

African (AFR) AF: 0.0162 AC: 674 AN: 41562

American (AMR) AF: 0.141 AC: 2162 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1010 AN: 5178

South Asian (SAS) AF: 0.0874 AC: 420 AN: 4808

European-Finnish (FIN) AF: 0.0932 AC: 987 AN: 10592

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0846 AC: 5754 AN: 67994

Other (OTH) AF: 0.0819 AC: 173 AN: 2112

Alfa AF: 0.0727 Hom.: 89

Bravo AF: 0.0746

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.29
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9332978; hg19: chr1-47407950;