rs4748417

Variant names:

• chr10-17737807-C-T
• rs4748417

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;