rs10517727

chr4-160831560-C-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 0.102 in 152,050 control chromosomes in the GnomAD database, including 870 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 0.10 (870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 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: 0.102 AC: 15463 AN: 151932 Hom.: 864 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.00639

Gnomad SAS AF: 0.0550

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0959

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

GnomAD4 genome AF: 0.102 AC: 15496 AN: 152050 Hom.: 870 Cov.: 32 AF XY: 0.0987 AC XY: 7337 AN XY: 74334

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0738

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.00640

Gnomad4 SAS AF: 0.0555

Gnomad4 FIN AF: 0.0782

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0972

Alfa AF: 0.0995 Hom.: 406

Bravo AF: 0.101

Asia WGS AF: 0.0310 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.15
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517727; hg19: chr4-161752712;