chr3-72466809-G-A

Position:

• chr3-72466809-G-A

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 0.456 in 152,006 control chromosomes in the GnomAD database, including 17,548 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 0.46 (17548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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: 0.456 AC: 69225 AN: 151888 Hom.: 17534 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.456 AC: 69253 AN: 152006 Hom.: 17548 Cov.: 32 AF XY: 0.465 AC XY: 34554 AN XY: 74280

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.461

Alfa AF: 0.508 Hom.: 16197

Bravo AF: 0.447

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11128275; hg19: chr3-72515960;