chr3-185638388-T-G

Variant names:

• chr3-185638388-T-G
• rs9878208

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 0.0852 in 152,174 control chromosomes in the GnomAD database, including 810 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 0.085 (810 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 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: 0.0852 AC: 12953 AN: 152056 Hom.: 814 Cov.: 32

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0881

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0571

Gnomad OTH AF: 0.0833

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

GnomAD4 genome AF: 0.0852 AC: 12960 AN: 152174 Hom.: 810 Cov.: 32 AF XY: 0.0886 AC XY: 6589 AN XY: 74394

African (AFR) AF: 0.0956 AC: 3968 AN: 41524

American (AMR) AF: 0.0883 AC: 1348 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5166

South Asian (SAS) AF: 0.329 AC: 1582 AN: 4814

European-Finnish (FIN) AF: 0.0522 AC: 553 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0571 AC: 3882 AN: 68006

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0620 Hom.: 452

Bravo AF: 0.0813

Asia WGS AF: 0.253 AC: 880 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9878208; hg19: chr3-185356176;