16-25555245-T-C

Variant names:

• chr16-25555245-T-C
• rs803491

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 0.969 in 152,308 control chromosomes in the GnomAD database, including 71,480 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 0.97 (71480 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 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: 0.969 AC: 147403 AN: 152190 Hom.: 71421 Cov.: 31

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.966

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

GnomAD4 genome AF: 0.969 AC: 147521 AN: 152308 Hom.: 71480 Cov.: 31 AF XY: 0.969 AC XY: 72144 AN XY: 74472

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.966

Alfa AF: 0.964 Hom.: 9000

Bravo AF: 0.968

Asia WGS AF: 0.996 AC: 3465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs803491; hg19: chr16-25566566;