chr10-49544407-G-A

Position:

• chr10-49544407-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 0.77 in 151,968 control chromosomes in the GnomAD database, including 45,382 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 0.77 (45382 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.812 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: 0.770 AC: 116937 AN: 151850 Hom.: 45383 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.770 AC: 116973 AN: 151968 Hom.: 45382 Cov.: 31 AF XY: 0.771 AC XY: 57256 AN XY: 74270

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.796

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.818

Gnomad4 OTH AF: 0.793

Alfa AF: 0.769 Hom.: 5459

Bravo AF: 0.754

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.082

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4453140; hg19: chr10-50752453;