10-93161308-A-G

Variant names:

• chr10-93161308-A-G
• rs4918664

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 0.152 in 152,188 control chromosomes in the GnomAD database, including 3,914 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 0.15 (3914 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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: 0.152 AC: 23146 AN: 152070 Hom.: 3904 Cov.: 32

Gnomad AFR AF: 0.0385

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.152 AC: 23165 AN: 152188 Hom.: 3914 Cov.: 32 AF XY: 0.164 AC XY: 12236 AN XY: 74390

Gnomad4 AFR AF: 0.0384

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.136

Alfa AF: 0.128 Hom.: 2187

Bravo AF: 0.161

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4918664; hg19: chr10-94921065;