rs4748417

chr10-17737807-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 0.0458 in 152,238 control chromosomes in the GnomAD database, including 236 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 0.046 (236 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0631 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: 0.0458 AC: 6966 AN: 152120 Hom.: 236 Cov.: 33

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0578

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.0530

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

GnomAD4 genome AF: 0.0458 AC: 6966 AN: 152238 Hom.: 236 Cov.: 33 AF XY: 0.0459 AC XY: 3419 AN XY: 74414

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0577

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0537 Hom.: 62

Bravo AF: 0.0417

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4748417; hg19: chr10-17779806;