chr16-86400947-T-C

Variant names:

• chr16-86400947-T-C
• rs8054124

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 0.232 in 152,108 control chromosomes in the GnomAD database, including 4,115 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 0.23 (4115 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 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: 0.232 AC: 35268 AN: 151990 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.232 AC: 35303 AN: 152108 Hom.: 4115 Cov.: 32 AF XY: 0.229 AC XY: 16997 AN XY: 74368

African (AFR) AF: 0.239 AC: 9897 AN: 41466

American (AMR) AF: 0.194 AC: 2968 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3472

East Asian (EAS) AF: 0.201 AC: 1036 AN: 5162

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4810

European-Finnish (FIN) AF: 0.200 AC: 2118 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16141 AN: 68004

Other (OTH) AF: 0.254 AC: 538 AN: 2114

Alfa AF: 0.236 Hom.: 2278

Bravo AF: 0.231

Asia WGS AF: 0.250 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Publications

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Other links and lift over

dbSNP: rs8054124; hg19: chr16-86434553;