rs72301

Variant names:

• chr16-57366699-A-G
• rs72301

Your query was ambiguous. Multiple possible variants found:

• chr16-57366699-A-G
• chr16-57366699-A-T

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 0.893 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.864 AC: 35891 AN: 41534

American (AMR) AF: 0.815 AC: 12464 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3224 AN: 3472

East Asian (EAS) AF: 0.726 AC: 3755 AN: 5174

South Asian (SAS) AF: 0.873 AC: 4212 AN: 4824

European-Finnish (FIN) AF: 0.919 AC: 9752 AN: 10614

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63753 AN: 68024

Other (OTH) AF: 0.897 AC: 1892 AN: 2110

Alfa AF: 0.919 Hom.: 108930

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
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs72301; hg19: chr16-57400611;