chr16-66293410-T-C

Variant names:

• chr16-66293410-T-C
• rs233551

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 0.935 in 152,262 control chromosomes in the GnomAD database, including 66,673 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 0.93 (66673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.935 AC: 142246 AN: 152144 Hom.: 66616 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.942

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.935 AC: 142362 AN: 152262 Hom.: 66673 Cov.: 32 AF XY: 0.935 AC XY: 69627 AN XY: 74444

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.942

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.927

Alfa AF: 0.913 Hom.: 34065

Bravo AF: 0.942

Asia WGS AF: 0.980 AC: 3410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.52
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs233551; hg19: chr16-66327313;