chr10-23145815-A-C

Variant names:

• chr10-23145815-A-C
• rs7893600

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 0.95 in 151,838 control chromosomes in the GnomAD database, including 69,183 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 0.95 (69183 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.991 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: 0.950 AC: 144083 AN: 151720 Hom.: 69136 Cov.: 29

Gnomad AFR AF: 0.957

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.997

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.950 AC: 144183 AN: 151838 Hom.: 69183 Cov.: 29 AF XY: 0.946 AC XY: 70115 AN XY: 74156

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.973

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.997

Gnomad4 OTH AF: 0.948

Alfa AF: 0.980 Hom.: 127555

Bravo AF: 0.930

Asia WGS AF: 0.798 AC: 2777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.031
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7893600; hg19: chr10-23434744;