chr10-44501863-G-A

Position:

• chr10-44501863-G-A

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 0.821 in 152,148 control chromosomes in the GnomAD database, including 51,375 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 0.82 (51375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.854 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: 0.821 AC: 124865 AN: 152030 Hom.: 51333 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.821 AC: 124963 AN: 152148 Hom.: 51375 Cov.: 32 AF XY: 0.824 AC XY: 61289 AN XY: 74398

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.841

Alfa AF: 0.832 Hom.: 7508

Bravo AF: 0.820

Asia WGS AF: 0.778 AC: 2707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.88
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7919766; hg19: chr10-44997311;