chr16-56956804-C-A

Variant names:

• chr16-56956804-C-A
• rs247617

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 0.291 in 151,994 control chromosomes in the GnomAD database, including 6,624 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 0.29 (6624 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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: 0.291 AC: 44171 AN: 151876 Hom.: 6618 Cov.: 31

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.291 AC: 44209 AN: 151994 Hom.: 6624 Cov.: 31 AF XY: 0.289 AC XY: 21505 AN XY: 74288

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.267

Alfa AF: 0.318 Hom.: 9329

Bravo AF: 0.289

Asia WGS AF: 0.223 AC: 779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs247617; hg19: chr16-56990716;