chr10-43072623-C-G

Position:

• chr10-43072623-C-G

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 0.356 in 152,006 control chromosomes in the GnomAD database, including 10,046 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 0.36 (10046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54068 AN: 151890 Hom.: 10026 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.356 AC: 54112 AN: 152006 Hom.: 10046 Cov.: 32 AF XY: 0.357 AC XY: 26512 AN XY: 74296

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.358

Alfa AF: 0.368 Hom.: 1326

Bravo AF: 0.354

Asia WGS AF: 0.359 AC: 1245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.54
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: rs732610; hg19: chr10-43568071;