1-168672824-T-C

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 0.765 in 152,108 control chromosomes in the GnomAD database, including 45,696 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 (45696 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 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: 0.765 AC: 116273 AN: 151990 Hom.: 45641 Cov.: 31

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.765 AC: 116382 AN: 152108 Hom.: 45696 Cov.: 31 AF XY: 0.756 AC XY: 56224 AN XY: 74350

Gnomad4 AFR AF: 0.924

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.759

Alfa AF: 0.772 Hom.: 6238

Bravo AF: 0.769

Asia WGS AF: 0.585 AC: 2038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.7
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538173; hg19: chr1-168642062;