chr16-56961078-C-T

Variant names:

• chr16-56961078-C-T
• rs17245715

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 0.106 in 458,552 control chromosomes in the GnomAD database, including 3,157 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 0.090 (843 hom., cov: 33)
  • Exomes 𝑓: 0.11 (2314 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0896 AC: 13629 AN: 152182 Hom.: 841 Cov.: 33

Gnomad AFR AF: 0.0205

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0967

Gnomad OTH AF: 0.103

GnomAD4 exome AF: 0.115 AC: 35166 AN: 306252 Hom.: 2314 AF XY: 0.118 AC XY: 20557 AN XY: 174464

African (AFR) AF: 0.0196 AC: 172 AN: 8756

American (AMR) AF: 0.145 AC: 3993 AN: 27450

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 1201 AN: 10756

East Asian (EAS) AF: 0.223 AC: 2094 AN: 9406

South Asian (SAS) AF: 0.147 AC: 8789 AN: 59834

European-Finnish (FIN) AF: 0.150 AC: 1949 AN: 12970

Middle Eastern (MID) AF: 0.115 AC: 308 AN: 2688

European-Non Finnish (NFE) AF: 0.0940 AC: 15049 AN: 160076

Other (OTH) AF: 0.113 AC: 1611 AN: 14316

GnomAD4 genome AF: 0.0896 AC: 13639 AN: 152300 Hom.: 843 Cov.: 33 AF XY: 0.0958 AC XY: 7133 AN XY: 74464

African (AFR) AF: 0.0206 AC: 857 AN: 41580

American (AMR) AF: 0.130 AC: 1985 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5180

South Asian (SAS) AF: 0.143 AC: 690 AN: 4826

European-Finnish (FIN) AF: 0.154 AC: 1632 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0968 AC: 6582 AN: 68018

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.0937 Hom.: 283

Bravo AF: 0.0853

Asia WGS AF: 0.189 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.5
DANN	Benign	0.94
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs17245715; hg19: chr16-56994990; COSMIC: COSV52364059;