chr17-21283048-C-T

Variant names:

• chr17-21283048-C-T
• rs10468608

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 0.335 in 151,986 control chromosomes in the GnomAD database, including 8,632 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 0.33 (8632 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.355 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: 0.335 AC: 50864 AN: 151868 Hom.: 8629 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.335 AC: 50895 AN: 151986 Hom.: 8632 Cov.: 32 AF XY: 0.336 AC XY: 24944 AN XY: 74274

African (AFR) AF: 0.301 AC: 12475 AN: 41434

American (AMR) AF: 0.324 AC: 4950 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3468

East Asian (EAS) AF: 0.229 AC: 1185 AN: 5174

South Asian (SAS) AF: 0.328 AC: 1577 AN: 4812

European-Finnish (FIN) AF: 0.388 AC: 4093 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24353 AN: 67950

Other (OTH) AF: 0.335 AC: 705 AN: 2104

Alfa AF: 0.341 Hom.: 34676

Bravo AF: 0.326

Asia WGS AF: 0.264 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.66
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs10468608; hg19: chr17-21186360; COSMIC: COSV57576566;