3-72343990-G-C

Variant names:

• chr3-72343990-G-C
• rs9832740

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 0.581 in 151,970 control chromosomes in the GnomAD database, including 26,476 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 0.58 (26476 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 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: 0.581 AC: 88227 AN: 151852 Hom.: 26444 Cov.: 31

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.581 AC: 88312 AN: 151970 Hom.: 26476 Cov.: 31 AF XY: 0.577 AC XY: 42848 AN XY: 74292

African (AFR) AF: 0.726 AC: 30080 AN: 41406

American (AMR) AF: 0.600 AC: 9173 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3468

East Asian (EAS) AF: 0.647 AC: 3345 AN: 5172

South Asian (SAS) AF: 0.549 AC: 2640 AN: 4812

European-Finnish (FIN) AF: 0.389 AC: 4108 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35135 AN: 67948

Other (OTH) AF: 0.599 AC: 1261 AN: 2106

Alfa AF: 0.549 Hom.: 2877

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.37
DANN	Benign	0.36
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs9832740; hg19: chr3-72393141;