chr10-44768973-A-G

Position:

• chr10-44768973-A-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 0.317 in 152,100 control chromosomes in the GnomAD database, including 8,012 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 0.32 (8012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48229 AN: 151980 Hom.: 7991 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.317 AC: 48283 AN: 152100 Hom.: 8012 Cov.: 33 AF XY: 0.316 AC XY: 23496 AN XY: 74372

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.309

Alfa AF: 0.281 Hom.: 7814

Bravo AF: 0.319

Asia WGS AF: 0.235 AC: 815 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256688; hg19: chr10-45264421;