rs16848610

Variant names:

• chr1-201454530-A-C
• rs16848610

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0475 AC: 1971 AN: 41514

American (AMR) AF: 0.0423 AC: 646 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.112 AC: 542 AN: 4818

European-Finnish (FIN) AF: 0.0293 AC: 311 AN: 10606

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0656 AC: 4458 AN: 67986

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0628 Hom.: 377

Bravo AF: 0.0541

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.016
DANN	Benign	0.45
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs16848610; hg19: chr1-201423658;