chr10-103367521-A-G

Position:

• chr10-103367521-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 0.406 in 151,516 control chromosomes in the GnomAD database, including 13,281 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 0.41 (13281 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 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: 0.406 AC: 61516 AN: 151396 Hom.: 13278 Cov.: 29

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61544 AN: 151516 Hom.: 13281 Cov.: 29 AF XY: 0.411 AC XY: 30457 AN XY: 74018

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.408

Alfa AF: 0.454 Hom.: 21937

Bravo AF: 0.391

Asia WGS AF: 0.514 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11191666; hg19: chr10-105127278;