rs16848610

chr1-201454530-A-C

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 0.0553 in 152,176 control chromosomes in the GnomAD database, including 263 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 0.055 (263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8381 AN: 152058 Hom.: 259 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0293

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0656

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0553 AC: 8413 AN: 152176 Hom.: 263 Cov.: 32 AF XY: 0.0550 AC XY: 4089 AN XY: 74394

Gnomad4 AFR AF: 0.0475

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0293

Gnomad4 NFE AF: 0.0656

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0637 Hom.: 296

Bravo AF: 0.0541

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.016
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16848610; hg19: chr1-201423658;