rs72301

chr16-57366699-A-Gchr16-57366699-A-T

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 0.893 in 152,242 control chromosomes in the GnomAD database, including 60,971 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 0.89 (60971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 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: 0.893 AC: 135891 AN: 152124 Hom.: 60928 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.893 AC: 135982 AN: 152242 Hom.: 60971 Cov.: 32 AF XY: 0.890 AC XY: 66202 AN XY: 74426

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.815

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.897

Alfa AF: 0.923 Hom.: 86426

Bravo AF: 0.882

Asia WGS AF: 0.777 AC: 2706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.37
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs72301; hg19: chr16-57400611;