chr3-123997005-G-A

Variant names:

• chr3-123997005-G-A
• rs7429448

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 0.143 in 152,138 control chromosomes in the GnomAD database, including 1,892 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 0.14 (1892 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21809 AN: 152020 Hom.: 1891 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.143 AC: 21820 AN: 152138 Hom.: 1892 Cov.: 32 AF XY: 0.150 AC XY: 11184 AN XY: 74382

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.163

Alfa AF: 0.134 Hom.: 236

Bravo AF: 0.145

Asia WGS AF: 0.361 AC: 1251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7429448; hg19: chr3-123715852; COSMIC: COSV68291971;