10-109211677-A-T

Position:

• chr10-109211677-A-T

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 0.0776 in 152,276 control chromosomes in the GnomAD database, including 644 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 0.078 (644 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11818 AN: 152158 Hom.: 644 Cov.: 33

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.0683

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

GnomAD4 genome AF: 0.0776 AC: 11815 AN: 152276 Hom.: 644 Cov.: 33 AF XY: 0.0772 AC XY: 5751 AN XY: 74450

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0548

Gnomad4 ASJ AF: 0.0576

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0236

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.100 Hom.: 98

Bravo AF: 0.0708

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17783561; hg19: chr10-110971435;