10-43068406-T-C

Variant names:

• chr10-43068406-T-C
• rs3026720

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 0.285 in 152,164 control chromosomes in the GnomAD database, including 8,094 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 0.28 (8094 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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 (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.285 AC: 43273 AN: 152046 Hom.: 8076 Cov.: 33

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.285 AC: 43334 AN: 152164 Hom.: 8094 Cov.: 33 AF XY: 0.277 AC XY: 20579 AN XY: 74392

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0924

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.279

Alfa AF: 0.204 Hom.: 5347

Bravo AF: 0.308

Asia WGS AF: 0.147 AC: 510 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	1.6
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3026720; hg19: chr10-43563854;