10-43024243-A-G

Variant names:

• chr10-43024243-A-G
• rs3123712

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 0.0676 in 152,306 control chromosomes in the GnomAD database, including 472 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 0.068 (472 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0971 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: 0.0677 AC: 10307 AN: 152188 Hom.: 472 Cov.: 33

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.0735

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

GnomAD4 genome AF: 0.0676 AC: 10300 AN: 152306 Hom.: 472 Cov.: 33 AF XY: 0.0653 AC XY: 4865 AN XY: 74486

Gnomad4 AFR AF: 0.0251

Gnomad4 AMR AF: 0.0641

Gnomad4 ASJ AF: 0.0848

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0391

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.0723

Alfa AF: 0.0799 Hom.: 72

Bravo AF: 0.0646

Asia WGS AF: 0.0220 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3123712; hg19: chr10-43519691;