3-72343990-G-C

Position:

• chr3-72343990-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.599

Alfa AF: 0.549 Hom.: 2877

Bravo AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9832740; hg19: chr3-72393141;