rs461785

chr16-65775141-G-Achr16-65775141-G-Cchr16-65775141-G-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 0.424 in 152,002 control chromosomes in the GnomAD database, including 15,604 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 0.42 (15604 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.641

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 (EAS) allele frequency at 95% confidence interval = 0.899 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: 0.424 AC: 64443 AN: 151884 Hom.: 15589 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.424 AC: 64484 AN: 152002 Hom.: 15604 Cov.: 32 AF XY: 0.435 AC XY: 32314 AN XY: 74292

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.501

Gnomad4 FIN AF: 0.589

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.447

Alfa AF: 0.457 Hom.: 31791

Bravo AF: 0.413

Asia WGS AF: 0.656 AC: 2278 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	0.45
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs461785; hg19: chr16-65809044;