rs254366

Variant names:

• chr16-65948886-T-A
• rs254366

Your query was ambiguous. Multiple possible variants found:

• chr16-65948886-T-A
• chr16-65948886-T-G

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 0.546 in 151,970 control chromosomes in the GnomAD database, including 23,417 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 0.55 (23417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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: 0.546 AC: 82842 AN: 151850 Hom.: 23396 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.546 AC: 82908 AN: 151970 Hom.: 23417 Cov.: 32 AF XY: 0.548 AC XY: 40655 AN XY: 74224

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.507

Alfa AF: 0.267 Hom.: 512

Bravo AF: 0.552

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs254366; hg19: chr16-65982789;