10-93604867-A-G

Position:

• chr10-93604867-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 0.0983 in 152,326 control chromosomes in the GnomAD database, including 1,390 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 0.098 (1390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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: 0.0984 AC: 14981 AN: 152208 Hom.: 1394 Cov.: 33

Gnomad AFR AF: 0.0403

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.0874

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0953

Gnomad OTH AF: 0.0941

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

GnomAD4 genome AF: 0.0983 AC: 14973 AN: 152326 Hom.: 1390 Cov.: 33 AF XY: 0.105 AC XY: 7814 AN XY: 74492

Gnomad4 AFR AF: 0.0403

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.0874

Gnomad4 NFE AF: 0.0953

Gnomad4 OTH AF: 0.0936

Alfa AF: 0.0889 Hom.: 131

Bravo AF: 0.0904

Asia WGS AF: 0.337 AC: 1170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11187549; hg19: chr10-95364624;