rs1948773

Variant names:

• chr16-55713034-A-C
• rs1948773

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 0.0926 in 152,150 control chromosomes in the GnomAD database, including 716 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 0.093 (716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.0927 AC: 14095 AN: 152032 Hom.: 715 Cov.: 31

Gnomad AFR AF: 0.0462

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0926 AC: 14086 AN: 152150 Hom.: 716 Cov.: 31 AF XY: 0.0948 AC XY: 7047 AN XY: 74374

Gnomad4 AFR AF: 0.0459

Gnomad4 AMR AF: 0.0924

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.105

Alfa AF: 0.105 Hom.: 846

Bravo AF: 0.0901

Asia WGS AF: 0.156 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1948773; hg19: chr16-55746946;