rs16955008

Variant names:

• chr16-81303074-G-T
• rs16955008

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.123 in 152,248 control chromosomes in the GnomAD database, including 1,246 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 0.12 (1246 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 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: 0.123 AC: 18745 AN: 152130 Hom.: 1242 Cov.: 33

Gnomad AFR AF: 0.0814

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.123 AC: 18771 AN: 152248 Hom.: 1246 Cov.: 33 AF XY: 0.128 AC XY: 9499 AN XY: 74452

Gnomad4 AFR AF: 0.0813

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.222

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.128

Alfa AF: 0.124 Hom.: 132

Bravo AF: 0.117

Asia WGS AF: 0.141 AC: 489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	18
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16955008; hg19: chr16-81336679;