3-186873214-T-G

Variant names:

• chr3-186873214-T-G
• rs7615090

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 0.212 in 146,658 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.339
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.212 AC: 31018 AN: 146554 Hom.: 4002 Cov.: 26

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.212 AC: 31048 AN: 146658 Hom.: 4004 Cov.: 26 AF XY: 0.211 AC XY: 15048 AN XY: 71390

African (AFR) AF: 0.365 AC: 14345 AN: 39250

American (AMR) AF: 0.175 AC: 2593 AN: 14780

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 444 AN: 3384

East Asian (EAS) AF: 0.301 AC: 1482 AN: 4928

South Asian (SAS) AF: 0.244 AC: 1115 AN: 4570

European-Finnish (FIN) AF: 0.136 AC: 1373 AN: 10066

Middle Eastern (MID) AF: 0.208 AC: 60 AN: 288

European-Non Finnish (NFE) AF: 0.137 AC: 9117 AN: 66516

Other (OTH) AF: 0.201 AC: 403 AN: 2002

Alfa AF: 0.176 Hom.: 1802

Bravo AF: 0.225

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.9
DANN	Benign	0.77
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7615090; hg19: chr3-186591003;