10-104086316-A-G

Position:

• chr10-104086316-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 0.92 in 152,172 control chromosomes in the GnomAD database, including 65,033 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 0.92 (65033 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 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: 0.920 AC: 139852 AN: 152054 Hom.: 65000 Cov.: 29

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.920 AC: 139942 AN: 152172 Hom.: 65033 Cov.: 29 AF XY: 0.919 AC XY: 68390 AN XY: 74394

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.944

Alfa AF: 0.982 Hom.: 93434

Bravo AF: 0.912

Asia WGS AF: 0.893 AC: 3104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1320448; hg19: chr10-105846074;