10-43073439-T-C

Position:

• chr10-43073439-T-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 0.809 in 152,242 control chromosomes in the GnomAD database, including 50,675 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 0.81 (50675 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.43073439T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123049 AN: 152124 Hom.: 50611 Cov.: 34

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.809 AC: 123176 AN: 152242 Hom.: 50675 Cov.: 34 AF XY: 0.802 AC XY: 59682 AN XY: 74422

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.758

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.792

Alfa AF: 0.788 Hom.: 7522

Bravo AF: 0.827

Asia WGS AF: 0.734 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505994; hg19: chr10-43568887;