rs10517727

Variant names:

• chr4-160831560-C-T
• rs10517727

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.129 AC: 5368 AN: 41476

American (AMR) AF: 0.0738 AC: 1129 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0951 AC: 330 AN: 3470

East Asian (EAS) AF: 0.00640 AC: 33 AN: 5154

South Asian (SAS) AF: 0.0555 AC: 267 AN: 4812

European-Finnish (FIN) AF: 0.0782 AC: 827 AN: 10580

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7139 AN: 67956

Other (OTH) AF: 0.0972 AC: 205 AN: 2108

Alfa AF: 0.101 Hom.: 453

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10517727; hg19: chr4-161752712;