rs16898325

Variant names:

• chr6-66461853-T-A
• rs16898325

Your query was ambiguous. Multiple possible variants found:

• chr6-66461853-T-A
• chr6-66461853-T-G

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 0.198 in 151,846 control chromosomes in the GnomAD database, including 3,872 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 0.20 (3872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29962 AN: 151728 Hom.: 3858 Cov.: 32

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.198 AC: 29995 AN: 151846 Hom.: 3872 Cov.: 32 AF XY: 0.202 AC XY: 14984 AN XY: 74200

African (AFR) AF: 0.0537 AC: 2230 AN: 41490

American (AMR) AF: 0.310 AC: 4712 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 752 AN: 3458

East Asian (EAS) AF: 0.527 AC: 2689 AN: 5106

South Asian (SAS) AF: 0.317 AC: 1522 AN: 4804

European-Finnish (FIN) AF: 0.206 AC: 2179 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15174 AN: 67910

Other (OTH) AF: 0.241 AC: 508 AN: 2106

Alfa AF: 0.195 Hom.: 410

Bravo AF: 0.203

Asia WGS AF: 0.414 AC: 1439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.4
DANN	Benign	0.78
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs16898325; hg19: chr6-67171746; COSMIC: COSV107166952;