chr1-32861080-G-T

Variant names:

• chr1-32861080-G-T
• rs16835198

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 0.295 in 152,122 control chromosomes in the GnomAD database, including 7,921 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 0.30 (7921 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44876 AN: 152004 Hom.: 7916 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.295 AC: 44887 AN: 152122 Hom.: 7921 Cov.: 32 AF XY: 0.297 AC XY: 22089 AN XY: 74364

African (AFR) AF: 0.0959 AC: 3982 AN: 41520

American (AMR) AF: 0.386 AC: 5906 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1007 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2472 AN: 5156

South Asian (SAS) AF: 0.363 AC: 1750 AN: 4824

European-Finnish (FIN) AF: 0.350 AC: 3696 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24952 AN: 67978

Other (OTH) AF: 0.320 AC: 674 AN: 2104

Alfa AF: 0.327 Hom.: 3682

Bravo AF: 0.291

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.7
DANN	Benign	0.75
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs16835198; hg19: chr1-33326681;